I played Persona 3 Portable mostly, but yes I do own FES and played an hour or two of it. Let's structure this.
Persona 3 Portable was awesome. I think of it as the most modern old Persona game, because of the ability to control your teammates' actions. For this reason as well, it is a little easier to play tactically. The combat is more complex than P4, mainly from having 3 DIFFERENT PHYSICAL ATTACK TYPES. WTF ATLUS. The Story is the best in the series, and I'll do my best to not spoil it for those who haven't played this game that came out in 2006. And was rereleased twice. Basically, you play as an orphan fighting shadows between 12 am and 1 pm. And that's all I'm going to say. The twists and turns in this game rival M Night Shyamalan. Play it for yourself. The soundtrack is godlike as always, and the changes as the story progresses really hit hard with context. Oh yeah, also P3P also has a female story side, which I need to play still. Which adds a ton of dialogue and different Social Links.
Persona 3 FES is a little more accessible than P3P, but the combat doesn't have Direct Commands, which suck. But, unlike P3P, FES actually has characters acting out scenes and exploration with character models, instead of a sprite talking all the time. Which isn't bad, but having the 3D models is way better. The inclusion of The Answer, an epilogue to P3, is one of the biggest selling points for P3FES, but I would say it isn't worth it. It's almost all grinding and little story, so just watch the cutscenes on YouTube or somethin.
All in All, Persona 3 has the best story of the newer persona games, but FES has the worst combat. Like the story is really good. Like really really really good. I'm saying play it. Like seriously play it. Do it. I give Persona 3 a 5 all out attacks out of 5.
Persona 3 Portable uses a cursor as a stand-in character model, and depending on what gender you choose, the color is blue or pink.