ship designs boring and too similar

[Suicide Junkie]

All of the AI ships need some sort of 'base' level repair to compensate for their lack of a 'character' with skills like you get. Different races could have different levels of ability in various areas, of course, like the Amonkrie having higher armor regen.

For my Mod, I have set things in the components so that shields provide their own regeneration even if you don't have dedicated regenerators... fairly slow, but shield damage is never permanent if the generator is still there.
I also gave 0.001 hull repair for every crew member on board. I added crew capacity modifiers to the crew quarters (naturally), bridge and med lab.
So, unless the ship is almost completely gutted already, they can slowly recover. A disabled shield generator gets fixed in a few minutes, assuming no other damage.

So instead of spending 10 skill points on hull repair, you could just add a 10kt crew quarters in order to house 50 more engineers