There’s at least two Mario-related writing ideas I keep coming back to:
One is simply a Mario story told in the style of one of the Paper Mario/M&L RPG games, with some overarching theme (time travel, fantastic voyage, love, etc.), allies, and more. I’ve been thinking about a theme of “legends” and “legacy:” long gone figures have shaped the new lands that Mario and friends visit, (for better or worse) and legends have the power to inspire or corrupt.
The other is Mario and friends in a “Doctor Who meets Spectacular Spider-Man and/or Transformers: Animated”-style “ultimate universe:” a stand-alone continuity that distills and adapts the stories and characters and worlds from Mario’s history into a cohesive serial (like a series of books or television episodes). We may meet some pre-villainy villains, but otherwise there’s no original characters: they’re all adaptations (or combinations) of existing Mario characters from different games.
The first arc of the series, for instance, (“World 1”) would have a pre-adventures Mario and Luigi meeting Peach for the first time, and through various shenanigans, end up with a “faceship” (Super Mario Galaxy 2) that they fly across the universe to try and find the missing fragments of the Mushroom Kingdom (and the toads living there). Along the way, they encounter other recurring characters (villains included) that Mario fans will recognize, as well as slowly revealing lore about exactly why things work the way they do in the Mario-verse.
Also, Bowser’s MIA, leading to all sorts of power grabs from the various members of the Koopa Troop, with Mario & Co. caught in the crossfire.