Zen, most of the 'Human only' stuff you have to research, the computer AI does handle most of it well. The biggest thing is for the organic engine parts, due to the fact that they regenerate se4 mistakes them for organic armor and you may see ships with 8 engines or a base with engines (just think of it as a creature with vestigel legs...). Most of the tech that drives the AI nuts I have put into research areas it will not use unless told to in the AI scripts. The other stuff (deflector screens, 1kt armor patches etc it will use just fine).
And any AI that has the '9999' option in the research txt file will research stuff up to its max level (ie will build ships up to 5000kt, use nanite armor etc). I have tried to keep this as AI friendly as possible, if only se4 kept to the 'one per ship' rule only and max engine rule than everything would be fine

(as it is give a component a 'bridge' ability and a 'armor regeneration' ability and you may see a ship with 6 or more bridges...ugh!)
Glad to hear you like it
