It's not that it's largely unnoticed by the player base as much as the player base never even encounters it. The community consensus on the best way to play the game is using WASD and the mouse, like one would play a first person shooter. The game's controls are also designed with keyboard and mouse in mind, leading to common misconceptions amongst some players. For instance, in order to slow down in SRB2, you have to hold the opposite direction from your current momentum, as if you're holding left while moving right in the 2D Sonic games, which is rather contrary to the way the 3D Sonic games handle this.
Personally I suggest you play SRB2 with whatever control scheme you play first person shooters with, such as WASD and the mouse, dual analog sticks like a console FPS, or even keyboard only (several of the developers play this way very successfully). Give it a little time to get used to playing a platformer with those controls and you'll find the game controls much better.
*never knew Mystic was on Retro too and flips out*
So it's a known issue, but never been a priority? Keyboard/mouse controls are simply not as relaxing for me to use, (Staying close to the keyboard for WASD, and lots of arm movement for precise turns with the mouse.) so I prefer leaning back with a controller for single player adventures. On top of that, there are a lot of jumps and landings on very tiny platforms that I can't make without analog mode.
It's largely a preference for me. I gave the keyboard an honest try while I waited to stock up on PC controllers again a couple years ago, my form was very stiff and sloppy for the whole two weeks. RTSs, and first-person shooters as far back as Doom, are where I prefer a keyboard, 3D platformers and racers are disastrous for me to play with one.
Can I blame not playing enough pre-Dualshock PSX platformers as a kid on this one? /> The controls in Croc and Tomb Raider were something else to adjust to.