So purple seems to be more popular in the Sonic community. I personally preferred his grayish blue design because it looked more realistic when he was with the other characters. I always thought his purple scheme made him stick out too much or made him look too bright.
That's actually one of the key principles which character designers follow when creating a cast of characters. By assigning each character a different color scheme, they instinctively become more recognizable to the viewer. The same thing applies to shape, personality and role. If it's done poorly, the characters would be less memorable. Part of me can't help but wonder if Rotor's duller color scheme was partly the reason for him being forgotten by some.
Sure, the grey/blue design might look more realistic, but this is a series that stars a blue hedgehog that can run at supersonic speeds. If the series was striving to be more realistic, they would've made Sonic brown and run at normal speeds - and that would've been boring. Had they stuck with the pilot designs, Sonic probably wouldn't have looked so out-of-place compared to the rest of the cast.