My enjoyment of ShtH stems mainly from the combat and platforming, 2 things hindered by how missions work. Now, I'm not against missions on paper. Giving the player a wider array of tasks to complete can make a game more replayable and fun. It's more what the missions are and how they're implemented. If I'm doing Dark missions, the game will still let be complete Hero missions by accidentally killing the wrong enemies, in a game with a focus on gun combat and a variety of fun weapons to use. It's BUILT to facilitate running through levels shooting enemies but severely punishes you for playing that way. Enemy alignments shouldn't have been tied to mission completion, they should've just been tied to the chaos powers. There are changes I'd make to those too but I wouldn't NEED to. Rather than defeating enemies of a certain type be a clear condition, JUST make the missions variations on goal rings, with non-tedious alternative versions of that. Maybe to complete a dark mission, you've got to steal a hidden key card and get to the goal ring. Or maybe for a hero Mission, you've got to rescue Cream from the Black arms by finding a secret path and getting to the goal ring there. There's a lot you can do that isn't a drain on dev resources but also isn't the tedious slog of the missions we got.
The core gameplay is fine, basically just a variation on Heroes' gameplay, it's the secondary and tertiary gameplay loops that hold Shadow back as much as it is. I like Shadow, with a HUGE asterisk. If we ever get Shadow the Hedgehog with mod support somehow, I'll fix the missions myself.