I think that in order to "fix" Bahamut you would just have to take out its need to stand close to the player. It could be like Garuda: standing somewhere and doing its thing without feeling it has to follow you everywhere. That's about it really, as long as you don't move and watch for animation clipping, Bahamut is alright.
I'm on the board of having Egis completely removed actually. Like making them work as stances that unlock abilities based on which Egi you choose, but everything would come from the Summoner, making weaving oGCD less of a pain without the pet's AI. (with flashy animations to make up for the loss of the ugly Egis)
Now it would be hard because you would need to rewrite all SMN quest, and that's not happening

but if Bahamut was fixed as I said and Egis worked that way, it would be a nice step for me.