Yeah I agree with everything there. There are a lot of good ideas in Sonic CD (mostly outtakes from Sonic 2, which was made by a different team) but most of them are poorly implemented, and the flow is nowhere near as good as the other 16-bit games. It does have its fans though, and Christian Whitehead is among them (hence Sonic CD having a disproportionately large presence in Mania) so I'm not sure he'd have wanted to radically alter the game even if given the opportunity.
The mobile ports of Sonic 1 and 2 are really good, if you don't mind the small screen. 16:9 widescreen, 60fps, save states, tonnes of bugfixes, Tails and Knuckles in both games, spindash in Sonic 1, Hidden Palace in Sonic 2... They really go a long way towards modernising the games.
Sadly emulation remains the only decent way of playing Sonic 3 & Knuckles though, which in my opinion is the best of the series. The Sonic 3 Complete hack does make some major improvements to it though.