Paper Mario: The Thousand Year Door
Paper Mario: Sticker Star
The "other" isn't really a true Paper Mario game in my book. And Sticker Star barely counts either...
Hopefully at E3 next year they could reveal a Wii U Paper Mario, but it depends how thinly stretched Intelligent Systems is with SMT X FE and Codename Steam and whatever else they are working on.
It was different, but it's still a Paper Mario game that had a pretty good story.