Fes.
Jesus christ the awakining is so lame in portable without animated cutscene and the beggning of the game in general is much more lame.
The psp lets you Control party members directly but the game was built around the ai party members so it's not bad as long as you actually use the commands.
Yeah the 3D may become pretty boring after some time but the 2D visual novel thingy becomes boring much faster and the scenes are so much better when you can see what is actually happening.
The epiloge "answer" is pretty bad but it's there in fes version at least.
Beyond the female protagonist (which is actually pretty good) there's not much else, like some teachers have a portrait now and there's an extra save point in your desk at school but you can live without that, there are skill cards now but they don't fit in p3 in my opinion, there are more Elizabeth quests but no one cares about that and there are apparently some refrences to persona 4 now but it's nothing ground breaking.
In short Play fes, and if you ever want to Play the game again you can Play female protag in psp version.