There's this helpful guide that contain a lot of what you can do in Geneforge 2, I recommend reading it. This Guide: https://gamefaqs.gamespot.com/pc/918441-geneforge-2/faqs/26410

Some things I found out:
Some areas occasionally damage you just for being there, but if you have enough resistances, their damage is not hurt you as much.
Most of these areas require energy resistance, so save equips with those resistances. Those red squares that hurt you with you walk on them are energy-based, so having enough Energy resistance allows you to walk on them safely.
Acid spraying traps can be hard to deal with when there are a lot of them (at least with you pick the shaper class), but stacking Acid resistances makes dealing with them manageable (I still suggest holding on to some healing and curing method just in case).

It appears that you can hold up to 30,000 gold at once. I didn't buy a lot of things from normal shop and eventually reached 30,000 while I still had things to sell, so don't be afraid to buy anything that might have some use, even if you are just going to drop them in a hoarding spot.
when you receive Exp from a quest and you have some creations or party members, they will receive some of the Exp too, so if you want all the Exp for yourself, I suggest removing all party members before you complete a quest. I think Exp gotten from unlocking things with living tool might be split to party members too (I imagine removing party members every time you get Exp can be kind of annoying).
I went through most of the game with 15 mechanics and still had 60~ living tools after once I unlocked everything, so maybe you don't need that much mechanics skill. the most living tools I needed to unlock something endgame was 15 tools, so maybe hold 30 tools if you want to drop some of them for weight reasons.
I noticed some doors are connected to 2 levers and sometimes, 1 of those levers require less living tools to unlock than the other lever (The locked doors leading to the final mandatory map are an example).
I think the more living tools you use to unlock something, the more Exp it give, maybe up to a cap of 50. Also maybe avoid getting keys that unlock things as those don't give you Exp like using living tools do.

I hoarded some Items I found because I thought them might being important in a future quest.
Gemstones and Emeralds: There's an NPC in the North corner of Fort Muck that will buy Gemstones and Emeralds from you. He Buys them a little cheaper than other shops, but he never runs out of money. I sold a few of these item to normal shop and I emptied them all out before I ran out of stuff to sell, so I recommend always selling these items to this NPC.
Iron Bars: There is a blacksmith around the center of Drypeak that will buy Iron Bars from you. Doing so will give you money and Exp.
Shaper Equipments: There is a merchant Lady in the Inn near the NE exit of Medab that will buy Shaper Equipments from you. Doing so gives you money and Exp.
Research Notes: There is a Blue Shaper in the Barzite-Only building in Gheth that will buy Research Notes from you. Doing so gives you Exp and I think money. However, you can only talk to him if you are allied with the Barzite, otherwise he will be hostile when you get caught inside the building he is in.
Named Books: Only 3 or 4 Named Book are need for Quests, I guess the rest can be sold to normal shops. The hardest Book to find is the Ember and Onyx Book, found only near the South corner of Benerii-Uss Entry. This Area will be hostile if you have not done some Taker Quests that might anger the Awakened, meaning you'll probably have to anger the Takers to complete this specific Book Quest.
Bolts of Cloth and Sheets of Paper: I thought an NPC might want these Items, but I never found such an NPC, so I guess just sell them to a shop.

In my run of the game, I wanted to join every faction at least once. Some quests and rewards are only available if you join a certain faction.
You have to talk to a faction leader in order to join their faction, and most of them will not let you join if your opinion is not leaning towards their side. The guide I recommended talks about opinion more. Basically, the opinions are pro-shaper and pro-servile. Some quests and conversation options changes your opinion value. I tried to complete all possible quests (even opinion changing quests) while avoid using conversation options that changed my opinion and I appeared to ended up with a pro-shaper opinion. Learned Darian in Darian's Sanctuary can heavily change your opinion one time.
Completing some faction quests be make other factions hate you and unjoinable, so you may not want to complete those quests if you want to join those other factions. Such Quests Include:
Attacking the Radiant College: Angers Barzites
Attacking Magus Complex or Stealing Awakening Information: Angers Awakening
Killing a faction's leader: Angers said faction

Having a high enough leadership level can allow you to skip the pre-entry quests you need to complete before officially joining a faction. I think skipping those quests makes you miss the quest completion Exp, so maybe do those quests anyways.
you get Exp when you officially join a faction.

I think joining a faction removes the Not Your status of most items in the faction's maps.

Servants:
Requires a pro-shaper opinion or high enough leadership to join, no pre-entry quests needed
I don't think there are any faction-only side quests for the Servants
Every major Servant quest will anger a faction, so you won't be doing much if you haven't finished up with the other factions' quests yet.
Angering the Servant will make it impossible to sell iron bar to the drypeak blacksmith.

Barzites:
Requires a pro-shaper opinion to join, 2 pre-entry quests needed that can both be skipped with enough leadership. These pre-entry quests should not anger any factions.
You can actually join the Barzites twice, once by completing the pre-entry quests normally, and a second time by using the leadership pre-entry skips. this will get you the faction joining Exp twice and a second chance at completing Barzite Quests (you'll probably need a pro-shaper opinion when you want to join a second time)
As a Barzite, Krogst in the mountain base map will teach you Quick Action 3 time for 2000 gold each time, be sure to do this before killing him to complete the hurt Krogst quest.
A shaper in the Barzite-only building in Gheth will buy Research Note from you, so try to sell as many of them to him as possible beofre you leave the Barzites (there were some Not Your Research Notes from other factions's maps I could not safely steal before I left the Barzite faction)
Commander Brent in Gheth and Selithra in Rising will give you minor Barzite-only side quests. These quests should not anger any factions, but they will 1 faction's trainer unavailable.
Every major Barzite quest will anger a faction.
Some Canisters can only be obtained by completing Barzite quest that will anger some factions, something to keep in mind (I think the canister were just some stat increases).

Takers:
Requires a pro-servile opinion to join, and 2 pre-entry quests needed, the second one is unskippable and will anger a faction.
As a Taker, Amena Blade in Zhass-uss will ask you to do a side quest, this quest will not anger any faction
The Taker quest will anger the Awakening and Barzite faction, but not the Servant faction (unless you slayed their leader).
I managed to attack the Benerii-Uss area without angering the Taker (Before I joined them) and it appears only attacking their leaders and other Drakon actually anger the Takers. If you want to join the Takers, I recommend saving in a friendly Zhass-Uss before trying any actions that may anger the Takers and try to not create another permanent save unless Zhass-Uss is still friendly. you might also kill some somewhat helpful NPC that will help you if you are a Taker, but will also attack you if you are not a Taker, so be careful if you decide to attack Benerii-Uss.

Awakening:
Requires a pro-servile opinion to join, 2 pre-entry quests needed, I think 1 is skippable and nither will anger a faction.
Some shops will only be available to Awakening members. Griffith in Triola, Teresa in Zhuss-Uss, and Mazrich in the Guarded Groves will give you side quests (Mazrich will be unavailable if you completed a certain Barzite pre-entry quest beforehand). I don't know if any of these quests will anger any factions.
I think Tuldaric in Magus Complex will alter you and teach you advanced spell (but not tier 3 shaping skills) as soon as you join the Awakening.
The first major Awakening quest will anger the Barzite, and then a later quest will anger the Takers.
Angering the Awakening will make it impossible to sell Shaper Equipments to the merchant lady.

in my run of the game, my faction joining order was Servants>Barzites>Takers>Awakening, but it appears I can join the Servant without having a pro-shaper opinion if my leadership skill was high enough, so maybe you can join like Barzites>Takers>Awakening>Servants instead. However, it appears joining the Awakening late makes you miss some of their side quests.
Possible Joining Routes
Pro-Shaper opinion>Barzite>Learned Darian changes Opinion to Pro-Servile>Taker (slay Barzite Leader)>Awakening>Servant
Pro-Shaper opinion>Barzite>Learned Darian changes Opinion to Pro-Servile>Awakening>Taker (slay non-Servant Leader)>Servant
Pro-Servile opinion>Awakening>Taker (slay Awakening Leader)>Learned Darian changes opinion to Pro-Shaper>Barzite or Servant>The remaining faction
Pro-Servile opinion>Servant (vie leadership)>Taker (slay Servant Leader)>Awakening>Barzite

I will talk about how I clear the Inner Gazak-Uss map as the Shaper Class and dealing with other difficult enemies.
I attempted Inner Gazak-Uss after I thoroughly explored all the other maps. I was a level 50~ Shaper playing on easy difficulty. I had 18~ Intelligent which gave me 1000~ essence, allowing me to max stat a Rotghroth to solo the map.
The only dangerous enemies for me in the map were the Eyebeasts and the Oozebeasts since they had an (apparently) unavoidable attack, especially since Eyebeast's unavoidable attack also has a very high chance of stunning your creations, making them very annoying.
My most important equips were the Stasis Shield and the Stabilizing Band, which protected my Rotghroth from the Eyebeasts' Stunning attack (I did still get stunned sometimes, but it was more manageable). The other equips were focused on making my Rotghroth as strong as possible.

First thing, there is a platform at the middle of the northwest edge that will spawn enemies periodically. The enemies spawned from this platform seems to know your character's location and will go straight there, sometimes walking pass your creation. I think this platform does not spawn anything when your character is near it, so I placed my frail player character here whenever I had my Rotghroth clear out the map to prevent possible ambushs. I don't think the platform ever runs out of spawns and can't be stopped permanently.

When I first entered the map, I kept my Character near the exit and send my Rotghroth down the south hall to try to thin out a group of 3 patrolling Eyebeasts. When you fight Eyebeasts, try to push them into a corner to prevent them from running away and using their stunning attack. I had my Rotghroth aggro 1 eyebeast, ran behind a corner and ambush it when it came around the corner. The other patrolling Eyebeast will be coming soon, so try to kill the first one quickly before they gang up on you. You also have to worry about being ambushed by a platform-spawned enemy during this phase of the map.
After you take out 1 Eyebeast, you can exit the map to healing up and save. When you come back, you can either try to finish the patrolling Eyebeasts or try to get your character to the spawning platform to temporarily stop it before sending your creation to the patrolling Eyebeasts. Finishing the Eyebeasts first risks you getting ambushed by the Platform enemies, while going to the platform means if your creation gets defeated by the Eyebeasts (I could only take out 1 Eyebeast before I had to retreat), the Eyebeasts will probably block the exit, making it impossible to retreat safely (maybe use some essence pods to create another creation to stop the Eyebeasts).
After you defeat the patrolling Eyebeasts (there might be 1 lone patrolling Eyebeast somewhere else on the map), you can send your character to the spawn platform to stop the spawns and send your creation to clear the rest of the map. Remember to retreat whenever you need to heal up and try to save right next to the exit to prevent creating a permanent save where you can't escape the map safely.
I think you want to clear the region around the platform first before you explore deeper in the map. South of the platform are some Rotdhizon, further south is a lake with Oozebeasts, you don't have to clear them yet. There is an Eyebeast and several Battle Gamma in the north corner of the map. When you decide to fight them, you want to trap the Eyebeast in a corner while making sure the Battle Gammas don't run pass your creation and attack the player character. The Eyebeast was the only thing that threaten my Rotghroth, so once it trapped the Eyebeast and got the aggro of all the Gammas, I had an easy time defeating all of them safely.
My Rotghroth had max Dexterity, so everything other than the Eyebeasts' stunning attack had only a 1% of hitting it, so I was mainly concerned with defeating Eyebeasts first.
There's a Rotghroth Spawner at the Southwest edge, protecting some shaping canisters.
I think there's an Eyebeast in the food room in the northeast section.
There are some Drakons and Rotghroth scattered around the map, I don't think they patrol the map.
There's a super Rotdhizon in the South corner of the map, try to lure it to the south bridge so you can fetch the gauntlet it drops without having to go near the acid pools.
There are Reaper Cores at the Southeast edge that are blocking the path to the Eastern corner.
At the eastern corner, there are 2 Eyebeasts, 2 Ur-Drakons and a Drakon Master. I Placed me Rotghroth right behind the corner leading to the enemy's room, saved there, entered battle mode, and try to get right in front of an Eyebeast to make it back into a corner. I would then try to kill that Eyebeast while hoping I don't get stun- or Slow-locked too much. If you failed to take out an eyebeast, just reload your save. If you take out the first Eyebeast, you can probably let your creation die and then try to retreat from the map quickly before any enemies ambush you.
When you come back, try to defeat the other Eyebeast the same way. once you have taken care of the Eyebeasts, you can start with the Drakons. The Drakon Master actually had a 10% chance of hitting my Rotghroth if it had a blessing. once you defeated the Drakon Master, the map become free to cross.


I hope my guide helps you enjoy Geneforge 2.