The problem is that they've forgotten that super speed wasn't the only thing Sonic had. They've also forgotten about how the original Sonic games had a really unique level design scheme in comparison to other platformers, along with the ball rolling physics used to explore them.
The 3D Sonic games are just one-way racetracks with generic platforming sequences peppered into them. They don't give you any freedom. You can't explore or stop moving on your own accord. Sonic Unleashed takes it a step even further and replaces some of the platforming with QTEs outright. It's barely even a game anymore.
The other problem comes from the constant need to add "variety" by introducing completely different game mechanics for the other characters. The whole point of other characters is to give them different abilities that allow you to tackle the same game in a different way, not shoehorn another game in there entirely (and even worse is that the make them required to see the end of the whole game).
Basically the whole design philosophy of the Sonic games has tanked as a whole.
Flawed with good reason? What does that mean?
It's like you actively LOOK for flaws in my posts to be sarcastic about. :|