I mostly (read:entirely) agree with you about the new special stages, but the decision has clearly already been made and apparently met with general consensus so I don't think there's much point in complaining now.
Yeah, I know, Sonic Team Junior probably wanted to show off their impressive coding skills (Nights stage is one of the most impressive things I've seen done in Doom engine, ever). Still, in my opinion, it just doesn't belong in a sonic game. What if the player doesn't know how to play Nights? I guess this part is explained in the manual, but when a fan of sonic plays a sonic game, he already knows how basic sonic gameplay works and can skip the manual (especially when new sonic games have in-game tutorials anyway). I've never read a SRB2 manual in my life and had no problems with the game, until now. Maybe a short in-game tutorial would be nice. A one-two screens explaining the basics of Nights gameplay, why not?
Also, for some reason I keep getting stuck on special stages and bouncing off the walls, which screws up the controls. A more clear level design and a few helpful arrows would be nice. Currently, Nights special stages are a mess and basically unplayable the first time you get to them. Also, Tails and Knuckles need their own sprites for special stages. The way characters turn into Sonic isn't working in context of this game.
A bad game design decision is still a bad decision, no matter how many years ago it's been made and no matter what focus groups say. I don't necessary say that including Night special stage was a
bad decision, but for me, it spoiled the game forever. Makes me wonder, why couldn't they release it as spin-off project... That would appeal to a lot of Nights fans out there and everyone would be happy.
If you're interested, not long ago I'd created a file called 2.0ss.wad that pretty much does what you want, and can easily be found by just searching for it, since I'm not sure if I could post a link to it here; of course it is a modification, so it will not allow you to collect the emeralds in a legitimate way, but I'm guessing you could simply download a savefile with the emeralds already collected if you really do not wish to get them through the vanilla game, ever.
This is a great news, thanks!