Honestly, I found some of the things you're praising Mania for to some of its weakest aspects, especially when compared to Sonic 3&K:
-While bringing back Blue Sphere is neat, what isn't neat is how drawn out and pace breaking it feels as a mini-game compared to the brevity of Sonic 3&K's. The fact that most of Mania's unlocks are tied to it doesn't really help it from overstaying its welcome either.
-Similarly, while I initially found "that" boss to incredibly interesting on my first run, on subsequent playthroughs I found it(and other bosses that are more gimmicky than fun) to be a massive drag to the point where I've started replaying stages in Time Attack just to avoid the tedium. This even bleeds over into one of the new Zones that wastes a entire Act to callback to an older Sonic stage that wasn't even fun the first time.
-The story in Mania...isn't what I'd call well or even cohesively told, even if we're taking the fact that there is no spoken dialog into consideration. The game can seemingly never decide if Sonic & co. are either: warped to the next Zone via the plot macguffin, naturally transition to the next Zone like in Sonic 3&K, or warped to the next Zone via...a fade to black like Sonic 1&2? The way Mania treats storytelling ends up coming off as so sloppy(and this isn't even getting into how anticlimactic and flaccid the ending is) that I question why they even bothered with a story in the first place.
Anyways, while I definitely agree that a new 2D Mario could stand to be a bit more inspired from an art style, level theme and music standpoint, I wouldn't say any of those things are exclusive to Sonic, much less Mania in particular. If anything I'd say Mario would be better off taking a page from the likes of Epic Yarn, Wooly World, Tropical Freeze or hell, just Super Mario Land 2 which had excellent and varied level themes.