The Special Stages as they are right now are, honestly my favorite in any Sonic game. Mania is a close second for how well it fleshed out CD's special stage style, and in a way, I feel that kind of mentality can apply here- the NiGHTS special stages are incredible fun, but they can be fleshed out further and improved upon, like the jump from CD to Mania.
I do agree that they are fairly long, but when you get into Dream Hill and Alpine Heights, the length makes sense as they're full stages instead of bonus levels. The main 7 levels can be shortened ever so slightly, as I'm happy with their length personally but I see why others find them too long.
Honestly, my major gripes are with how it's very very easy to miss spheres and rings by a few pixels and how some look visually.
If the spheres slightly gravitated towards Sonic, like when you get the Nightopian Helper, you could focus more on speeding through the stages and get that awesome feeling of flight from the original game- compared to getting angry at Dusty Canyon and Magma Caves for missing just one sphere and missing out on an emerald because of it.
Speaking of Magma Caves... it could get a serious visual overhaul to use assets from the main game better, and not blind me with redhot lava- which hides a few flame hazards partway in and that kills my runs in that level far too often, either because I need to go exceptionally slow or I hit fire that I couldn't see clearly- and both cut down the timer. As for other stages visually, they could benefit from slopes and maybe easier to see hazards.
The other stages are just fine, difficulty-wise. For example, Egg Satellite is hard as hell but in a fun way- you can clearly see the lasers (which for the record, you can bounce off them at specific angles without taking damage), and the shrinking gimmick is neat! I however have yet to play Black Hole, and apparently that one is too hard for far too many.