There's a female MC, who has her own social links (mostly male party members) Fusion spells are much harder to pull off, the dungeon design (backgrounds) are slightly different. The big draw is the FeMC route, and full-party control, you sacrafice the answer, the presentation, and a few other elements. There's also a super easy, and super hard mode to make up for the party control, but without being able to abuse fusion spells it's a real pain. Whether it's worth it to have the guys as s.links, and the other stuff is up to the individual, I vastly prefer FES.
The ending can be very slightly different, and it takes P4's approach to s.links, with only Star on FeMC's being able to be broken. This means it's actually possible to max all 21 without a day-by-day guide... Kinda.
If you're new to the series or play P4 first it's very hard to go back to FES. Also FES just got a PS2 classic release so if you've got a PS3 you can grab it for $10 anytime. Go with whichever you feel better about and good luck.
Edit - Revalations Persona was hackjob, and that one you're almost 100% better of going with the psp remake. Although people have complained about the remixed music.