As for the Bowser fight, who is to say that we have to use the original Bowser? I have been thinking about ways to adapt the Heavy Press boss
I made some while ago. What if I redrew it to some kind of giant Thwomp, replaced the giant eye with a window showing Bowser controlling it, and added in a homing bullet generator or something? And I have an idea for a cutscene that could be right before the boss:
[Sprites shown: Mario, Bowser]
So you are here at last. You might have gotten past my armies, but I am ready.
[Sprites shown: Mario, Bowser inside the thwomp boss]
Prepare to lose that y-axis of yours to my new secret weapon, the [insert name of boss here]!
Jesus freaking hell. It's stuck in the ceiling.
Oh well. That was just a demo.
Initiate weapons cycle, authorization Koopa alpha omega.
[Heavy Thwomp lights up]
And yes, that cutscene would be perfectly doable with Romi's cutscene tool.