Paper Mario was killed because the significance of story was considered a bad thing... I wonder how long Mario & Luigi has...
Miyamoto was supervisor on Dream Team, and it's got lore and backstory (though, notably, it doesn't have any moments where it unironically tries to be sad, like SMRPG and the PMs did), so maybe they're backing off on that. Or maybe they're testing to see if Dream Team sells better than Sticker Star, and the winner decides whether Mario can have stories.
Also, on the not offending anyone note, it's interesting how the Mario & Luigi games occasionally lightly imply that Luigi's gay or bi (there's his crush on Peasley in SSS, and in Dream Team, there's a point late in the game where one male character wants to "nap on" another male character, and Luigi cheers him on with a ^o^ face while Mario looks shocked. Also that scene takes place in Luigi's subconscious.).