Oh boy, I've got plenty here!
I've got some Bowsette/Super Crown game/Hack ideas that would be a good idea to work out. Initially, an SMB3 ROM Hack replacing Bowser with Bowsette was what I was gonna suggest...until I did it and am adding MORE to it. So here's some of the others I have too, mainly a Bowsettevania game which is sort of a mix between Castlevania and Zelda 2.
I'm keeping this spoiler free, please note me if interested in more. See below:
The background setting could be something like Castlevania (Peach's Castle) using the SMB3 palette since there's so many castle and tower designs in that game anyways, wouldn't be hard using SMB3 layout. As for enemies, would be a up to someone to decide on whether Toads, Yoshi, etc. Speaking of Castlevania, it could even be more like the 3rd game where you have different allies with attributes. Like Boosette able to float/move through certain walls (like Invisible cap), Chain Chompette being a strong weapon once unlocked (like SM:RPG). There would be those giant SMB3 chests all over the castle to collect things in too.
I'm pondering, if maybe Boosette can be made a playable character, would considering giving her some 'legs' but probably not. She can float and hover for short periods of time. Can spook enemies to stun and pass by them. Stunned enemies you can walk past so that'd get rid of issues of tight corridors. Boosette would be able to hide/go invisible like in the Paper Mario games Lady Bow in order to prevent damage. Think of the stone form of the Tanuki suit. Once unlocked, she can be swapped out at a save point. Instead of fire breath or Bowsette bomb, Boosette's specials (same as SMB3 Bowser, can break blocks) can spook to stun enemies and lick to damage.
Other -ette characters can appear in the game to provide support, like if you can rescue some of them, they'll open up a shop for you (Kamette/Goombette) or health items from others like Koopas. Also hidden chests and secret items/weapons so exploration would be more encouraged.
Similar to maybe Zelda 1 or 2 where you gain health by beating bosses. Exp points from enemies and bosses for Kamette's shop. Coins used for currency at Goombette's item shop. Allows you to switch characters at will like Castlevania 3 if using a partner system. Maybe swap at just save points if only Bowsette and Boosette. When Bowsette (or Boosette) start losing health, they lose clothing too. At 1/2 health the skirt comes off, then when only 1/4 left, the stockings are gone and she's bare legged. Could even see about removing arm bracelets to make it appear more 'naked' in this regard.
The same blocks would be used over from SMB3 so it'd still kinda have that Mario aesthetic. So you can hit question blocks, regular ones, hidden blocks (Boosette can easily find), and pipes. Late game will allow warp pipes to visit different areas of the castle for fast travel I'm pondering if after every boss a warp pipe opens up and it takes you to the foyer. Keys would definitely be a use here. The castle would be set so you would need a key in order to advance to the first 2 bosses and then allow branching paths for like the next 3 maybe so you can pick and choose which you want to face next.
-Piranha Plant whip
(shields - can't be used while 2 handed weapons equipped)
-Metal Mario shield
-Candy (magic gauge)
-Full chicken (full health)
-As a bonus, Mario's or Luigi's notes which would briefly give hints to some secret areas or how to beat bosses. Probably would work better if Capt. Toadette's treasure hunting notes.
-A Kamette potion shop for health/magic (for skills like fire breath), if you get enough skill exp you can use it to level up or upgrade weapons or make your consumption or skills take less. To refill the gauge, it's by defeating enemies by jumping or using weapons on them.
-Maybe have a Goombette weapon shop, one did in SM:RPG so why not? It'd better give coin collecting more of a purpose than.
-Have Koopa Troopa save points.
To go even further beyond, consider giving limited inventory and to have one of the regular/smaller Boosettes (or Lakitette) store some items. You can get them all around the castle like Resident Evil. Probably better if in the Goombette item shop to have that option to [buy, sell, store].
Was thinking one of the bosses could be Pink Gold Peach from the Mari Kart games. Somewhat like a liquid shadow of a shamed princess (or Liquid Peach, kek). And have some secret bosses.