No game features cripple the AI; what you are seeing is that SE5's stock AI is even more poorly developed than SE4's. Its theoretically capable of handling everything in the game, but the code isn't there yet. Kwok has made a lot of progress in BM's AI, for example. He even has it doing remote mining now, something impossible in SE4.
The new combat system is definitely noticeable in multiplayer games, as it is far more than just a "3D" change. The real time execution is the important bit, as it eliminates all of the idiosyncrasies of SE4's ultra-primitive phase-less combat. Combat resolution is certainly slower in strategic mode though, as Aaron has not yet figured out how to compute it at the speed of math (as opposed to a sped-up real time clock).