Well, at least it was a cool twist at the time for Bowletta, and it made a lot of sense for Bowser to face his perfect match in BIS. Shrowser was an asspull though. I would be more fine with Bowser being the main villain/final boss of Dream Team if Antasma wasn't introduced as a red herring for folks who wanted a new villain. And Paper Jam yeah one of many instances of huuuuge potential of something epic that relates to the many adversaries of both M&L and PM but using just Bowser in the 2 styles merging instead. But that whole game was full of missed opportunities so I wouldn't say the final boss in particular was notable for that.
This series gave me my favorite villain and even character in the franchise, and the biggest sins it has done are killing him off and Paper Jam. I'd love a Wario and Waluigi appearance, but IDK, I think they'd work better as either recurring troublemakers ala Popple or a parallel "adventure" of their own ala Bowser in BIS. Donkey Kong I'd definitely prefer as a protagonist (like BIS Bowser but not as rude). Wart would've made a perfect boss in Dream Team, and tbh they could've wrote the plot to have him enter the plot instead of Bowser, team up with Antasma and even later betray him, and it wouldn't feel as bitter because Wart hasn't shown up as the final boss in every damn game, most notably the latest ''RPG'' at the time raising question on whether non-Bowser villains would ever come back.
Similarly Tatanga could've appeared in PIT and allied with the Shroobs. I think I'd prefer to mostly stick with new villains for the series, at least for the main villains. M&L's villains have usually been really interesting (much like old Paper Mario, same with other character roles, explaining why I find PJ so wasted) and unlike Paper Mario it hasn't abandoned this direction (i think... actually can't be sure since we've only had remakes since PJ, but I'd like to say we're out of that uncertainty now, at least for M&L. If only we could get out of it for both)
Since Fawful is canonically dead (as I'm legally obligated to admit and acknowledge... grumble) I still hope they find a way to tap into his popularity in less story-reliant contexts. They can't keep him alive retreading old ground forever, as much as I'm enjoying this remake period. At least some merch would be nice Nintendo tbh.