Nintendo did a pretty good job with characer roles for Mario characters around the GameCube and DS era what with Luigi and Peach getting their own games and Yoshi receiving a sequel to Yoshi's Island with Wario and DK's infant counterparts making surprise appearances (okay, Baby DK's apearance wasn't really a surprise since he was in the commercial). But yeah, after that, Nintendo's Mario stories kind of went back to Bowser kidnapping Peach.
Baby Luigi said:
Have Nintendo make a plot where Peach doesn't get kidnapped for once? Sounds like a great plan to me.
Super Mario Bros. 2
Luigi's Mansion
Super Princess Peach
Super Paper Mario (okay, she got kidnapped at the beginning, but after that she was playable throughout most of the game)