I Spose Shadow and Silver do somewhat count as Protagonists and Antagonists as they have those moments in the games they feature in, however what Robotnik says holds true of those two, but then again in my own personal opinion the only Sonic "Crew" that have any depth are Tails, Knuckles and Amy (Sonic is obviously included in that list) Robotnik himself has depth but I wouldn't include him in the Sonic Crew.
The problem with the topic at hand is that there is so many it can be near countless some by design like in say Dungeons of Dredmor where you are just some one sent to kill off Lord Dredmor, Like in Torchlight 1 or Diablo 1 and 2 (Cant speak for 3 I have not played it)
Or by accident like in Quake 4 where they tired to get you to give a crap about Caine but really you still felt as generic as the doom guy
Spoiler warning:
