According to Koji Kondo, the reason we haven’t seen Baby DK since Mario Super Sluggers is because shortly after the game’s events he died of Sudden Infant Death Syndrome (SIDS).

FACT: This particular Mario pose makes him safe for insertion

The manual of Paper Mario: The Thousand Year Door confirms the popular theory that Mario’s motivation for the game’s plot is driven by the guilt he felt from the weight of his action’s at the end of the previous installment.