Personally I'm all for the idea of making Brak the DCZ boss and having something new for the standard final boss (BCZ3). S3&K back in the day had a final boss that had multiple phases, none of which lasting overly long but still presenting a fair challenge. I'd like to see SRB2 do something similar with BCZ3 in which the player makes use of what they've learned throughout the game to put Eggman in his place, with him perhaps growing more desperate as the fight progresses, and maybe even leading up to a chase sequence in which Eggman is trying to escape. I'd say each phase should be around 2-4 hits each, and the fight consisting of 3 or 4 total phases. Ideally, it shouldn't recycle previous boss fights. However, I wouldn't be against the idea of Eggman finding different ways to use the same old machines or combine them together. I'd prefer something totally unique though.
If Grand Eggship Zone or some other Super Sonic battle becomes a thing, I'd personally prefer they find some kind of way to make use of Super Sonic in 3D. I know the idea of a NiGHTS style boss fight is rather popular, but personally I'd find it rather jarring to have played through the entire game in 3D only to have the true final battle taking place in 2D. I'm not against such a boss fight existing, but I'd rather that get pushed aside to a separate NiGHTS mode unlockable rather than being part of the main campaign.