Sixty seconds with the controller and you'll understand. My specialty in fan gaming is 3D physics, so I'll describe a couple of specifics.
Characters' turning is immediate and not gradual, yet slowing to a stop is still very gradual. This makes it difficult to control one's direction and to stop in a particular spot, and creates a horrible disconnect between player and controls. Jumping does not conserve horizontal momentum; in other Sonic games when you jump you still go the same speed, but in '06 you're slowed to a max speed. There is also no way to slow to a horizontal stop while jumping, thus forcing you to rotate in circles just to stay in one spot.
These two details alone could have done SO much to fix the game's feel, and it would only take an hour or so to do. But there's yet more.
Instead of nice ground detection, they had to revert to a "tag" system. As long as you touch something tagged as walkable, you will stand on it at the exact angle of the ground, even if it's a ceiling and you're standing perfectly still. This would have taken a few days to fix, maybe. If the folks hadn't done a platformer before.
The game has no momentum, and the controls are weird as hell.