I wish Mania had brought back the special bonus stages that alternate depending on your ring count from S3&K. It was the perfect fusion of fun new Doilus Stages, older physics gimmicks and an expansion of the "50 Rings to get in" limitation. Combining the rotating maze Special Stage from Sonic 1 with Casino Night's Pinball motif was a stroke of genius. At the very least, I'm glad that the Mania team brought back elements like Glowing Spheres and the Gumball bumpers for Titanic Monarch. Makes me wonder if they'd initially planned to include those kinds of stages and rejigged it into regular level gimmicks once they settled on the Blue Spheres medallion conceit. Given the iterative implementation of Special Stages becoming Bonus Stages, I don't think I'm going off-topic by talking about them. But I think my favourite Special Stage has to be Blue Spheres. Partly Nostalgia since Sonic 3 was the only one I owned as a kid (had to rent the other), but it's still genuinely fun, and still a challenge to this day. Though I'm certain the Mania ones had a difficulty spike. I like that they cribbed concepts from SegaSonic Bros. to the point of specifically using it's music. It's always fascinating to see the progression and the retooling of older concepts into new experiences. Sonic 2's Special Stage definitely annoyed me though, especially with Tails' lag. Why lag was ever a thing in a quick time obstacle run, I'll never know. Perhaps it was implemented better in the PC port of 3D Blast because I still look at those stages fondly.
Personally I feel like the sonic cd special stages are probably my favorite, they're just fun to play for me.
