I'd say, Partners in Time.
Why?
Super Mario RPG took 12 years to finally get released over here, which make many people not care about this game anymore, as releasing SNES games in a Wii era is like selling a Pentium II PC in the year 2037.
Paper Mario is a good candidate, but I never managed to beat it.
Superstar Saga was good, a great world, and such. It used to be my favourite.
Thousand-Years Door is a game I want to play some day, but even now, a second hand costs € 60,- everywhere, which is even more than a brand new GCN game costed, back then. I don't want to pay so much for a second hand game, as I'm not supporting anyone by doing this.
Partners in Time added lots of interesting mechanics, not seen in Superstar Saga. It made SS put on the second place. Only to bad PIT was so linear.
Super Paper Mario is not even a true RPG game, move on!
Bowser's Inside Story made me go like, "Nintendo, really, that's enough.", I didn't like the idea of being inside Bowser, controlling him all the time like a friend, and then end up battling him.
Sticker Star had a unique concept of not attacking, but using Stickers in battle only, but it didn't feel alright. The battles were way to easy and linear, this way.
Dream Team isn't even out yet, so let's skip that one.
