I have some thoughts about this also...
First of all, the point of repairing stuff is to repair stuff, not to make things invulnerable. With reintegration you are talking about a T2 ability which lets the ship repair itself. If it was buffed too much, it would need to be moved to T3 or possibly T4.
I agree with the useless bonus for Vasari colonizing. It could be made more useful, iirc it doesn't even scale for levels except for it's duration, which is kinda lame.
It seems that Vas scouts capping neutrals should be nerfed somewhat, since they easily get very imba in maps with lots of neutrals and are pretty hard to catch if handled properly, unlike colonizing frigs, for example. (maybe restrict Vas scouts limit to 4-5, or increase capturing AM requirement by 10-20, or reduce antimatter capacity from 300 -> 200, or raise fleet cap req from 3 -> 5, etc.)
I find it kind of stupid anyway that there's just some totally invulnerable omnipotent resource extractors just sitting somewhere in deep space. Why not just make them neutral asteroids on which colonizing frigs / scout ships could actually build destructable extractors? Then maybe make it possible to build static defense next to them? Or make them upgradeable for a cost so they could have their own little turrets! (and possibly become tougher)
Deliv engine aint that big of a deal. Kostura could be made more useful, though.
edit: I just noticed you weren't really talking about capship abilities but synergy... Well, how about running around with a dozen carriers with the Marauder's speed boost for example? 
i think u have to play the other races for a while, and than think about balance
I agree with him also, your perspective seems to hold only the Vasari view.
There's a whole lot of information to be taken in before trying to make balance suggestions.