the transition from 2D to 3D was notoriously difficult and many 2d era franchises died from the increased dev cost and a poor grasp of 3D game design. Most of those titles were cut from the same cloth as Mario, but Sonic had a unique crop of issues to contend with. Because of the speed sonic games run at you needed a longer draw distance and far more actual level to play in. Mario could get away with simply dropping you in a box filled enemies and obstacles and call it a day, while Zelda only had to worry about the immediate room. Sonic had to have a long, linear track that was fun to run through and skillful at the same time. Sonic just barely crossed the finish line with adventure, and it had quite a few advantages going for it. For one, Sonic was a first party dev for the dreamcast so they got direct support and knew the ins and outs of the hardware they were working on, as well as a fair bit more money backing them. they also were dealing with far more advanced hardware as they skipped over the ps1/n64 era other properties had to navigate. Even so, Adventure cut a lot of corners to get where it got. Graphical fidelity was low and texture quality was worse than some PS1 games, the few places there were real textures anyway.
The biggest problem with sonic was the fact that levels were, by necessity, brief. to run through a single level won't take more than a few minutes. That was fine on the genesis where arcadey games were the norm but by the dreamcast the industry had changed and games were expecting to be bigger and more time consuming. Mario got around this by having multiple objectives in a sandbox, which wouldn't work for sonic as we'll soon see. Adventure's answer was to have multiple playable characters who ran through slightly altered stages. Individually these stages didn't take very long but cumulatively they'd come out to something worth your cash. The other advantage was a more in-depth story which is largely responsible for the sonic fandom we know now.
This system mostly worked, though fans disliked the gameplay styles of some of the characters, namely Big the Cat who lacked the speed aspect entirely and required a different skill set. Adventure 2 had fewer playstyles (only 3 compared to 6) but greater differences between them. More importantly, levels in adventure 2 were based on the same 'template' visually but had unique layouts. For example, Knuckles and Shadow both have levels with pumpkin towers, but one is at night and the other is during the day. this cuts costs for asset creation and doesn't feel cheap. as a kid I actually thought it was super cool to see the same locations from different perspectives. Still while the speed levels were praised, the other playstyles weren't so well received, and sega continued to experiment. Sonic Heroes saw no difference in play style between characters, but still required you to finish all teams which made for an extremely repetitive experience. Furthermore combat encounters were added and lengthened to give the new engine more time to load in assets and to keep the game stable graphical fidelity took a big hit. the lack of any real story made these issues more prominent.
Shadow The Hedgehog was the fourth iteration of 3D sonic games and in many ways had the best answers to the problems listed above. The game had one playable character with one playstyle, and had an abundance of levels built from similar templates. 22 levels with unique layouts compared to the 16 or so of it's predecessors was a nice improvement. Combat encounters returned but with the addition of gunplay they were far less annoying to get through. The story got a bigger focus and could be influenced by player choice. It was altogether a solid design. The problem was, in order to advance to certain stages you needed to complete certain requirements. a 'hero' mission, a 'neutral' mission, and an 'evil' mission though some levels only had 2 missions. This opens up some cool ideas but the missions tended to be very boring and repetitive. 'kill all the good guy', 'kill all the bad guys', 'scour the level for tiny collectibles'. The game did everything it could to slow you down to lengthen gametime without ever being fun or engaging. furthermore repetition reared it's ugly head. In order to get the true end, you needed to play the first level of the game a minimum of TEN TIMES, as there's only one starting level and you can't skip it. You needed to fight all 10 final bosses and get all ten endings, but there were only 3 final fights, half of the time you were fighting egg dealer. The game also had vehicle sections that were poorly programmed and barely worked, and ultimately the game was still programmed in the Heroes Engine which wasn't a fun time.
Sega would continue to iterate with Sonic 06 but as that game had such fundamental problems any greater design decisions to alleviate these issues is lost in the shuffle. Unleashed made the most strides by having a proprietary engine that looked extremely slick, and prioritizing the sheer sense of speed over control or challenge, but unleashed cut it with subpar action game segments. Colors mostly fixed the sonic formula by accepting the series was ultimately going to sell no matter what and emphasizing it's arcade-y roots, but I think there was a lot of potential in the shadow solution. having more intuitive missions (like 'complete the level in x minutes' or 'don't get hit more than 3 times') and more starting levels could do a lot to make sonic a more dynamic experience again. Right now we have no news on the blue blur's next title, but sega has confirmed it's in development and that '2021' will be a big year for the brand. I'd love to get a mania 2 next year in the meantime and see sonic return to it's more experimental stage.