Battle Network is great. The grid system by itself is nice in that battles often have some execution challenge in dodging and positioning yourself for attacks. Chips are nice in that the RNG avoids that you can rely on one strategy and have to try different chips you might not necessarily use otherwise, sometimes even putting you at a disadvantage. The style system in 3 is a nice touch in particular, since that means your options rely on how you play, which differentiates playthroughs. Beautiful.
I haven't played any Paper Mario in a while, but Thousand Year Door's system was nice if a bit simple after a while. Stylish hits and crowd management were things I found neat about it.
Lately I've been playing Deus Ex Human Revolution. Only thing about it that seems RPG to me is spending points on augments, but some of them do let you do things differently over others like jumping high or carrying heavy stuff (some of them are probably obligatory though for all I know). I like how it forces different play styles, although some of them seem like some sort of easy mode, mostly the stealth ones from what I've seen. Haven't finished it but I'm pleasantly surprised so far.