From an AI developers perspective there is little difference, the AI in GAE is in need of a revamp to handle all the new features, and I am planning such a revamp, but was going to work on improving the multiplayer first, though I'm now thinking this will probably be decided by a poll.
Since he hasn't yet, I figured I'd beat him to the punch so that the community can decide which would be more important to do FIRST (we can assume both will come in time, though obviously one must come first).
Personally, I would prefer to see the AI worked on, because it cannot use some of the new features, such as it won't build a unit with a water field, nor will it EVER use subfactions, among others. Unsure yet if it can use the carrier units that GAE 0.3 will offer. Regardless, the multiplayer works, but the AI is "broken" and thus, I think we would benefit more from that AI. Let's not go overboard immediately though. While things like Lua AI's are very tempting, they might be a bit too complex, and it may be better to just get a simple, working AI that can handle all the new features of GAE functionally.