Agreed on the autoResolve vs RTS, it would take a lot for the AI to adapt (it would need a killer focus fire algo, and positioning algos to make the best of own and enemy fleet capabilities).  It wouldnt be the Manhattan Project however.  SD2 AI during RTS does a pretty decent job.  Its weakest part it focus fire.

However, if I had a wishlist, it would be to create ships like in SD2.  I'm right brained, not left.  I would enjoy doing that, hoping to optimize ships, rather than spending time on how my ship looks, which is inconsequential to gameplay.  Granted, the base engine for ship design they have built will lead to MANY cool 'looking' ships and races which I hope are shared with the community, which by far is the biggest factor in its replay-ability strength.

While I like the shipyard I wish the components had more depth of meaning in the game. And yea fluff is nice but compared to what other things the game needs, they could have spent less time on that and more on AI/completing a few hundred other items.