Having skim-read some of the posts, I stumbled upon the one that reflected my opinion the most.
The one by Neo about the game being changed when you use a certain character.
SRB2 (The core set of levels) are designed with STK in mind. I know this is redundant, but bear with me. And there really lies the problem of the character suckage. The whole game is revolved around them, their abilities, etc. Even the weapon system could be considered like that: A rail can counter a constantly flying Tails, goddam fast rings because the characters themselves are goddam fast. Although this argument falls kinda short since, for example, counter strike has near instant hit bullets, and the characters are slow as mollases, but that's a whole different playstyle. SRB2 is revolved around being fast and fluid. If you strive away from the formula, your character will not be fun in SRB2.
The Doomguy in srb2. That would suck major balls, and I don't think I need explaining this. The opposite applies too. Playing Doom with Sonic would be a borefest. But they basically share the core character structure, stats and all that.
Mario 64 works because the game is designed with his moveset in mind. Alter the moveset, and you'll get obliterated.
SRB2 too, since it has the core mechanics set in stone for STK. Alter that formula, and you're gone. A character slow like the doomguy wouldn't make it out alive against a good patch of crawlas.
Solution? Who says custom characters can't be saved, but my real proposal is, create interesting levels with them in mind, because the mainstream stuff just isn't designed for them. Even the loew jump height of Knux felt a bit last minute slapped into ERZ2 as a way to have a path specifically designed for him. (Please don't shoot me devs, I'm honestly sure this plan was set in motion long ago, but it felt kinda rushed in IMHO.)