OC mods are fine but I don't really think they should become vanilla characters, for a number of reasons. The chief reason being that it comes at heavy risk of bringing SRB2 deep into "Cringy fanfiction" territory. While one could argue that it is already in fanfiction territory, I feel that the limited story we have actually fits pretty neatly into the kind of thing one would expect from a Classic Sonic title. A totally new OC character however might be taking things a bit too far. Additionally, it would come with the question "Why does this character make it in but (Insert OC character here) doesn't?".
In regards to how a Super Sonic final boss could be handled in SRB2, I think a number of things are totally valid possibilities:
NiGHTS style - Probably the most obvious. It could work well but it would be something of a departure from the 3D nature of the rest of the game. It might feel more natural if more 2D sections are implemented into the main campaign.
Invisible Floor - The weakest option in my opinion. While this would play the most like typical gameplay, it also comes at the risk of feeling rather disappointing unless the fight is exceptionally designed around the usual playstyle so as to make the player not mind much. Nonetheless, there's enough potential to this one that I wouldn't shun the idea entirely.
Free flight (Egg Reverie style) - The option I am most fond of. For the most part I would prefer the free flight be limited to the boss fight, but I wouldn't mind if they put an enabler for it in Pandora's Box. This is the style that gives the player the most freedom of movement, and as such makes them feel more powerful. This would do the best at capturing the feeling of playing through Doomsday Zone in 3D. The ability to unlock the free flight alongside the other cheats in the Pandora menu would also provide extreme incentive to actually collect all the emblems without completing the task being overall mandatory.
Combination (Phases) - The idea of bosses that have multiple phases isn't a new thing, even to the Sonic franchise. Sonic 3&K had several bosses that were multiple phases, and the Advance series made pinch modes popular within the franchise. To combine multiple ideas into one in the form of phases that each play differently could be something of a double edged sword, as while it could end up feeling more epic to the player overall, it also comes at the risk of either the fight being too long, or each phase being too short lived. As such, this is the option that would most need to be handled with care, and would probably require the most work.
All that is my two cents, anyway.
