Short answer: Persona 3 FES
Persona 3 FES is considered the best version of Persona 3. It has both story chapters, The Journey, and its continuation, The Answer.. this is something Persona 3 Portable did not have.
Not only does P3F have these two story chapters, there are also tons of additional content such as new clothes, skills (i think? Cant remember) and what not.
However one "flaw" from P3F is that it still uses AI teammates so if youre not into that, then you may have to be patient.. unless youre planning to play on PC, to which i hear you can mod it so that you can Direct Control your teammates.
P3P on the other hand, is well... the lite ver of P3. There are no full 3D cutscenes except for one or two occassions. Only the dungeon segments are 3D.. the non dungeon segments are just top down isometric views with little 3D models around to interact. Also it does not have The Answer. However! You can play as a Female version of the Protagonist and there will be differences in POV in the story