Well I guess it depends on what you want more, the enhanced story of FES, or the enhanced gameplay of P3P. From what I gathered, FES is persona 3 with an expansion to the story on it continuing after the original game. P3P doesn't have the anime cut scenes and are instead just using in game engine, and P3P's gameplay is better than the previous version with full party control and other little things.
I dunno, I wouldn't be surprised if ATLUS released FES DLC for P3P later on seeing as the game is appearently selling really well and the UMD just didn't have enough space left on it to include FES with everything else. But that's just wishful thinking, but I wouldn't mind paying 5 bucks or something for FES DLC.
Again I guess it really boils down to whether you want more story or better gameplay. Playing it on a portable isn't bad, I really don't get why people get fussy over the screens, my eye sight aint perfect but I manage jsut fine. Anyways, if you wanna take the game wherever you go and enjoy it, get P3P; but FES may be better seeing as it's got more story and you probably can find it for cheaper than what P3P is at right now.