There are MANY things, just check the main site for them. I'll list some for you, anyway:
- Battle Frontier - new ways of battling
- Able to get BOTH Groudon and Kyogre
- Some plotline changes that make it a bit more different than RS
- Cellphone function like on GSC
- Rematch Gym Leaders! (only after E4)
- Able to get BOTH fossils
Check out the main site for more.
Hope I helped.