First, welcome to the forums. Hope you stay longer than many other people have.
Second, I like your boss battle idea, but it seems to be focused mainly on multiplayer. I didn't spot any kind of battle after Bowser for just single player, so it seems like it'd lead right to your 'Choose the door' scenario. I would suggest, for those playing single player, adding a fight against some clones of Mario, so it's similar to the multiplayer battle.
Also with the endings, I like the 'Choose a door' scenario. Just some things about each:
Master Allison wrote:Choose the cake as your reward:
Princess Peach appears from behind the door, very distraught!
She gives one terse indictment as the screen fades to black,
"You should not have done that! (Zelda Reference)"
I had to look this reference up (It's a reference to a Creepypasta around Majora's Mask, for anyone who's too lazy to look it up), and I'm not too sure if many people will get this reference. I think she should say something else, maybe another quote that's more recognizable, but I like this ending idea overall.
Master Allison wrote:Choose the princess behind the door:
Mario knocks on the door...
but to the player's suprise toad answers, (Mario jumps back in suprise) and shares a couple of moments of silence interrupted by Peach:
"Toad, who is it?"
Another couple of moments are spent as the screen fades to black and Toad says to Mario (rather embarressed),
"Sorry Mario, but your princess is in another castle."
*The door slams shut and Toad disappears within*
This one is kinda dark, but I like it. The "princess in another castle" joke just fits in to this ending. (Might want to make it a bit more PG though. Mario game, after all.)
Overall, a good idea... however, I think it's been said in this thread
that Maurice was just gonna be making his own ending instead. Not to bash this idea, because it is pretty good.