This is an extremely controversial take, even by "criticism of Sonic Mania" standards, but I think the biggest flaw of Mania was the lack of any slow-paced Marble Zone-y stages. I absolutely love those sorts of zones because you can memorise them and eventually play them just as fast as the other zones.
My second biggest problem with Mania is actually a little less controversial but also a little contradictory to what I just said, I feel the bosses. despite their visual spectacle and deep cut throwbacks, are too slow, with no method to get through them faster. (other than iframes, which IMO don't count) Spark the Electric Jester handled fast paced platformer bosses better IMO.