I'm curious, regarding the AI, are there any plans to give the AI an actually sense of alliances, because as far as I can tell, all an alliance actually is is a NAP. Until the inevitably break it (which they always do unless your quick killing everyone else).

As in, I was in a losing fight, and my "ally" jumps a huge fleet to that battle, so I'm all, "hurrah, reinforcements...wait, where are they going, they're jumping away..." and they go right past the fight. I lost that planet because the AI didn't act like an ally.

Also, are there any plans to be able to give basic commands to your AI allies, in the same regard as Rise of Nations did?

Yep, much more time will be spent on AI development. For the moment, if you want it more difficult than the Hard option, put multiple AI's on the same team so they won't fight each other and will only fight you. As for not helping you in the reinforcement, that looks like a bug - he should be reinforcing you (if he determines its in his best interest). AI commands will eventually be given by using the ping button.