Silver is the Modern Era's rival boss in the console version as well. They used him instead of Knuckles or Blaze because you have rescue them and there weren't any other characters that would've been appropriate. I'm guessing they didn't see much reason to change things for the 3DS version. Also, if just Silver's presence angers you, just wait until you see the first level of the console version's Modern Era.
I'm so happy Sonic's awesome again. I've been playing Sonic & All-Stars Racing Transformed recently. Excellent Mario Kart clone, probably the best game I've played all year. Chronicles...eh. It's an alright RPG, the dialogue is pretty good, but the enemies in the second half of the game are real assholes, the soundtrack is awful and the ending is kinda bullshit. Still, the game is fun enough.