1) Male or Female Protagonist
The female main character is a new take on the same basic story, but with two new characters and different people for Social Links. In other words, more story.
2) P4 Battle Improvements
Persona 4's battle system was practically the same as P3's but with a few tweaks that really made it shine. P3P carries over some of these improvements such as:
- Full AI Partner control
- If you're hit by your weakness and knocked down, the next turn you get back up AND can attack in the same turn
- Co-op attacks: Every so often after you knock down an enemy, your partner will ask to team up on one more enemy for a guaranteed critical hit. Good for enemies with no weaknesses.
- Guarding: I don't know why they didn't think of this for the original or FES. Guarding reduces damage and protects you from being knocked down by your weakness for one hit.
- Partner Equipment: You used to have to talk with each party member individually to change gear, but now it's all done on the main pause menu.
- Restoration (more of a downside depending on who you ask): One good thing about the original and FES is when you return to the main dungeon's entrance, you're fully restored. Now you pay a fee, I guess to keep from long grinding sessions, despite the characters having a fatigue system not present in P4 when paying to have Spirit restored showed up.