To help my gamethrough, I made notations of the items, upgrades, and obstacles I found.

UPGRADES
Stats Upgrades
Raise the respective status by 1

Abilities:
Skills that help the exploration, usually helping to reach places that you previosly couldn't.
Weapons:
tools that helps in both combat and exploration

ITEMS:
Life Can
Colored Keys

OBSTACLES:
Tech Door: Open with the Tech Shot mod
Rocket Blocks: Can only be destroyed using Rockets. The more darker they are more level of the
Boomb Blocks: Can only be destroyed using Bombs
Beam Blocks: Can only be destroyed using the Beam. The more darker, more higher is the level required.
Metal Blocks: Can only be opened using the Magnet skill.
Colored Locks: Needs a corresponding colored key to open
Charge Doors: Needs the Generator skill to open
Rapid Doors: Needs the Rapid Shot upgrade to open

obs: Whenever a X is preceded of a letter that means a skill of the corresponding letter is needed to get / reach it.

Aside from my notations, the game itself presents some basic information on the maps.
S = save points. Keep in mind that whenever you save the game, you can recover all your health.
Red rooms = the Boss rooms - although there is some of them that aren't marked on the map.

Here is the general diagram os the areas of the game.

The surface of the planet has some living creatures, and a cavern with tunnels that leads to some ancient ruins underground.
Here you can find a lone Life Up upgrade that not appear on the map - near the entrance - only accessible with a Beam Lv2 upgrade (gotten after the Starcore Event)

The Trine army made their base here.
There is a hidden Life up upgrade in the vertical section in the room just after where you get the Map.
Also, it's the area where you'll do most of the game's backtracking!

This area looks like a testing laboratory with some colored discs on the walls.
There is a hidden Shot Power upgrade in the same room where you get the Rocket skill.

Proceeding deep underground from the surface caverns, you'll find the crystal caverns, that goes even more deeper, reaching the magma area.

This place is where you find the other two weapon skills - aside from you own shooting weapons.

Beneath the crystal caverns is the Magma Base, that can only be accessed with heat shield .

The Star Shrine lies passing the magma base and is where the Starcore is kept, (and where ends the first half of the game).
It's the shortest area of the game, and where you'll upgrade your Beam to lv2.

The deeper area of the Star Shrine are straight-forward. There is no enemies here (aside from the boss).

The sequel of the Area 05. Here is where the Trine kept most of their weapons - which now are being used by the Omni.

Passing after the laboratories, are the computer controls of the Trine base.

As you proceed, through the enemy base, the defences becomes even more thougher.
This is where you get the last weapon upgrade (Beam lv3).
Keep in mind to do one last backtracking to get the remaining items and stats upgrades, before going forward to tnext area.
WARNING!!
There is glitch here that mess with the soundtrack fusing all sound soundtracks of any area you pass after reach here. To fix it, just save in the area you are in, and reload your game - for the sound track that area return to normal.

No more Trine cyber-technology. You reach the bizarre bio-organic base of the Omni.
Here you'll find the last upgrades you can get before the game's end.

The deep core of the Omni base. This where you'll fight the game's last boss.
WARNING!! WARNING!! WARNING!!
There is a GAME-BREAKING bug here: Whenever you get a key USE IT RIGHT WAY to open the corresponding door. If perhamps you get more then one key - the first key will be REPLACED by the last key you get!
So, to prevent a SOFTLOCK do as I said - or don't save AFTER get a second key (this way you can still reload your old save).