I'd have to say the Paper Mario series, as the plot and characters in these games were both innovating and fresh. Many of the Mario RPGs in particular seem to have broader storylines, from what I've seen.
Super Mario Galaxy was also good in terms of graphics, gameplay, and an overall unique concept that was mixed with your generic Mario storyline (aka "Bowser kidnaps Peach... but this time, in space"). I also loved the scenery throughout and the creative boss battles. Both Galaxy installments seemed to be successful due to this.
I also like the New Super Mario Bros. franchise, in part because they're fun, entertaining, and great multiplayer. :)
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