One is that I like is the concept of terrain doing stuff. Disgaea's geo panel system and La Pucelle's dark portal system both add to the complexity of the game in a mostly managable manner. Especially in La Pucelle, where I haven't hit a situation where you need to interact with the dark portal system to clear a level (excepting the tutorial levels). So it seems like the portal system is 100% optional, but beneficial if you decide to mess with it.
I like game mechanics like that, especially the ones that give you good dividends if you do manage to master them. I've been contemplating adding a CCG mini-game to Seventh Star like Xenocards from Xenosaga, with uncommon items as incentives. I've been turned off tying unique items to minigames ever since FF-X and the stupid chocobo racing game you need to power up Tidus' ultimate weapon. I'm thinking something like FF-VIII where you could refine cards to get items.
On the other hand, the geo panel system seems to add a little more variety to levels, which doesn't hurt.
Oh, and the second thought after playing La Pucelle was: just because it's fantasy doesn't mean it can't have guns.