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This topic has been pinned, so it's probably important 
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I'd recommend trying to play as a mechanitor to get a feel for it, the upgrade process is a bit arduous, but worthwhile.
I have uncovered several serious bugs, all related to this Mod, after a long time of searching. They variously break at World generation, Pawn generation, and so on. I have successfully confirmed that this is the Mod causing them to fail.
Also, in the Hugs Library Log, you will see a lot of errors related to a Meercat Pawn. They have nothing to do with this Mod and went away when I deleted the Meercat from the game.
This is my Hugs Library Log: https://gist.github.com/HugsLibRecordKeeper/e3fe0d190b8c4e9c257dfe19610feee8 .
I can't see anything explicitly related to Zeta Reticulans here, and considering you have *574* mods active I hope you understand why i'm doubtful it's Zetas causing an issue.
Did you just add Zetas to the list before the error popped up? Do the errors not pop up unless Zetas are in your modlist?
Is your pawn named "Lucretia" or "Gray" a Zeta Reticulan or a Hybrid?
Edit: I have one patch that could conceivably cause an issue in regards to thought state, but again i don't see it mentioned in the errors. And my test runs of Zetas in my much smaller modlists are error free.
Edit2: Looking at the Hugs Lib log again it seems the first errors start at a mod that uses "VFEI" as it's acronym.
"Could not find a type named VFEI.CompTargetEffect_Recruit
Could not find a type named VFEI.Verb_CastHumanEffect
Could not find a type named VFEI.CompTargetEffect_Tame
Could not find a type named VFEI.Verb_CastAnimalEffect
Could not find a type named VFEI.CompTargetEffect_EraseInRadius
Could not find a type named VFEI.Verb_DoEffect "
And that's just the start, there's a lot more errors from different mods. There's no practical way for me to determine if my mod/code is something I should fix-up when your modlist is this chunky and exception filled.
As for Gray and them, yes, those are Zeta Reticulans, and I know your Mod caused that because I did the halving gauntlet and narrowed it down to your Mod. However, the Skill thing is NOT from your Mod.
Can you recall the name of the mod you're using that effects the Disfigured/Ugly/Pretty beauty trait?
DisfiguredAmeliorated
UglyAmeliorated
Don't appear to be related to Rimworld's core files, at a glance through the XML.
Using HARs base system, no custom patches from me, I have it set so Zetas don't get thoughts related to other pawn's being Ugly/Disfigured/Pretty nor is the "Beauty" trait allowed to spawn on Zetas themselves. To me this hints that you're using a mod that changes how beauty works which doesn't play nicely with HAR, just most HAR races don't limit the beauty trait/thoughts so it's not usually something that would be detected.
Edit: There's also a chance it's related to a Harmony prefix i did to thought states so if they're 0 they still show up on the thought list for Zetas, but im leaning away from that currently
Also, I have confirmed that the error with Skills is NOT from your Mod. Rather, it is from the Malay Mod. I messaged its author.
Fair assumption
If you mean there's a bug that limits *all factions* to 1 base then this isn't something i've seen. If you run the mod by itself on a clean list it should clarify whether the issue is this mod or not.
If you mean you only see a single base from *this* faction that would be because the faction generation weight is 0.12 with a minimum of at least 1 base set to spawn. On smaller maps/low population generations only getting a single Zeta settlement isn't unusual.
Firstly: the race description for the Thrumkin Hybrid is a repeat of the Forsaken Hybrid's description.
Secondly: the Moyo Hybrid's harvestable blood mechanic is, of course, only present when you have the Moyo mod active, but "Moyo-From the depth" is deprecated and development now continues under the name "Moyo2.0-Blood stained business."
Moyo 2.0 being active does not provide Moyo Hybrids their blood. Granted, "from the depth" has been ported to 1.5 and 1.6 by another modder, but I think full compatibility with the current official release would be nice. (Also, the updated "from the depth" mentions in its description that it implements the bloodbags differently, so probably also not out-of-the-box compatible with your mod in this sense.)
I can't replicate this, tested on both version 1.5 and 1.6. Was their a specific type of hybrid that was running into this problem?
I don't know if you can read C# but this is the patch that dish out the thought once the surgery is complete. It's simple and direct:
Also I added support for the new Moyo mods, just taking the time to remake the Thrumkin textures before the next update.
Edit: Okay I see, the label and thought icons are correct but the descriptions are swapped. Thanks for the heads up. There's a lot of writing so it's helpful to get someone who's actually reading stuff to give feedback.
Could not resolve cross-reference to Verse.ThingDef named AEXP_Hippopotamus (wanter=raceList)
Possible Matches:
[Source: Zeta Reticulans [Player/Hostile Factions]]
[File: C:\Games\Indiv\Rimworld\Mods\2241841840\1.6\Defs\RaceStuff\GDZR_Race_Short_Base.xml]
https://gist.github.com/HugsLibRecordKeeper/f12a44c63fc79b88f2a07afbd6164df8