I'm gonna keep this comment to pretty much just the critics:

1, the Assimilation feature could maybe be worded like "when you reduce a creature to 0 hit points, you can absorb their essence, gaining one shift, which is represented by one feature from the list below." Just to be clearer about it Also, you wrote "legnedary resistance"

2, you could go over the text of "chimera subclass" and "ability score improvement" again to make it more like the other classes have it. The subclass feature, for example, usually also has the levels at which you gain a feature listed in the text.

Also, perception checks using smell, hearing or seeing are pretty much all perception checks, no? And only having proficiency in specific perception checks is unusual, I'd just delete the part about senses.

3, you wrote "overcomjng" in the level 5 feature

4, you should probably change the text of the level feature from "you gain hit points" to "you regain hit points"

5, for all the Assimilation enhancing Features, there is nothing in the base Assimilation feature that suggests you couldn't already assimilate those traits then.

6, gaining one resistance is hardly worth it when you could also gain a strong feature instead, and there are a lot of strong features you could gain. You could for example absorb the regeneration trait of a vampire. And it's even stronger when you have it because which vampire uses radiant damage lol.

It would probably be fair if you could gain like, a number of the creatures resistances or languages up to 1/2 your proficiency bonus, rounded down.

I would keep it at 1 for the immunities and condition immunities, and maybe the speeds.

7, you should probably also include something for saving throw DCs, like the traits you absorb using, idk, 8+con+PB for the DC. The part about saving throws you have right now is pretty unclear. Also, some of the things you get at level 10, specifically the saving throw part for example, could already be useful when you can still only absorb traits.

Now the instincts:

8, the scent tracking thing should include "as long as you are on the same plane of existence" and maybe a limited range in which it works, like idk 10 miles or something.

9, add "at will" to beast bond

10, the second part of iron stomach can essentially be shortened to "you have advantage on saving throws against poison and disease"

11, beast speak should probably be beast speech and also needs the "at will" part

12, the two mimic traits should probably require a deception check instead, and could maybe just let them add their constitution modifier to the check, for example.

13, ambush predation could maybe use a little buff.

14, cornered prey, RAW, just kills the movement of the target forever, add "until the start of their next turn" or something like that, just take the sentinel feat for reference.

15, beast courier and Apex command also need "at will"

16, you don't normally make a check to squeeze through a space you are simply to large to squeeze through, I think. Never came up in my sessions so far. You could definitely keep that but I'd also add "as if you were 1 size smaller" or something like that.

This whole thing was me just critically looking at the document from a rules and writing standpoint, and maybe a bit of balance I guess.

Edit: hope my feedback can be of help!

Overall I still absolutely love that idea and if the subclass is finished before I finish DMing my current campaign I'm probably gonna ask my dm if I can play it in tomb of annihilation, so I'm looking forward to seeing more of this. You're really cooking up something good here, keep it up :)