Most Japanese RPGs use this save system, and it's pretty awesome. The most it'll do is change some dialogue and keep your stats, money, skills, etc. Basically anything that's dynamic. The latest one I've played allowed you to continue your levels from the last game and even threw in a bonus skill.
PSP did the same with Monster Hunter 2, and it was pretty cool as well. They gave you vouchers in the game you can trade in for extra items and stuff.
Don't know if this is the route they're taking from here on out, but it would be awesome to see a lot more variety in games like this.