Well, I explained my problems with them generally up above. Mainly an issue of the pace slowing down considerably, plus a new physics engine that can be hard to manage, leading to molasses gameplay in combination with not entirely feeling I'm in control of Sonic. Then you layer the breathing timer on top of that (complete with the most harrowing and evil retro timer music ever devised,) and the overall effect can be unpleasant at times. There are times when I die in the water levels and don't feel it's completely my fault. I think to myself, "I bet I wouldn't have made that mistake if I were using the above-water physics." Or "that bubble spawned exactly a half-second too late, causing me to die. Not sure what I could have done in that situation."
I'll fully admit to being dogshit at Sonic games. I'm not suggesting the games should be made easier. But maybe future titles could include an aquatic character, sort of like how Mighty serves as an easy mode for Sonic Mania's combat challenges. So if you struggle to deal with enemies or bosses, you can just pick Mighty. He has his own downsides though (no drop dash, slower progression, no flight) so it's a trade-off. Maybe players who don't like the underwater levels could pick "Mannfred the Mallard" or whatever the fuck, and he'd have more movement options in water. But still the same emphasis on the timer.
There are times when I just think the underwater levels become too slow, too plodding and too oppressive for their own good. I'm sure that's what some people love about those levels though.