Evil / Kinda Sorta Bad But More Good Some of the Time doppelgangers eh?...
Mega Man = Bass (Could argue Proto Man...)
Pac-Man = Pac-Devil (EXTREMELY Obscure)
Sonic = Shadow (A.K.A Original The Character: DO NOT STEAL), Metal Sonic
Mario.... = Wario, Metal Mario (Since Mario Kart 7), Shadow Mario, Robo Mario (look it up), Cosmic Mario, Cosmic Clone Mario. (I Gave up after that...)
I don't know what you guys are talking about so this means nothing to the thread, I just wanted to point this out for randomness sake.
Not to mention:
Link - Shadow Link, that guy at the end of Link Between Worlds I don't want to say for spoilers.
Pit - Dark Pit
Luigi - Waluigi
Pikachu - Raichu (Or Dedenne, Or Pichu, or Pachirisu, or Electabuzz)
Jigglypuff - Clefairy (Though I think Jigglypuff is the sinister version)
Meta Knight - Galactica Knight. Or Dark Matter
Kirby - Shadow Kirby... or Meta Knight
Dedede - Shadow Dedede
Captain Falcon - Blood Falcon
Peach - .....Wapeach? Daisy?
Dr. Mario - Dr. Luigi (with Death Stare Rx)
Villager - Tom Nook. The worst villain in video games.
Bowser - Dry Bowser. Bowletta. Dark Star Fused Bowser from Inside Story.
Little Mac - The guy from the SNES game!
Zelda - Hilda, Princess of Lorule
Ganondorf - Yuga.
Rosalina - Walina... Give it time.
Yoshi - Boshi, Birdo, Reaper Yoshi (The Grim Reaper's skeletal dinosaur steed with a living tongue. I may have made him up)
Fox - Wolf
Falco - Leon? Katt? Dash?
Lucario - Mewtwo. Granted this only makes sense cause of Smash Brothers. Really Pawniard or Gallade are the dark or opposite versions of Lucario.
I'm sure I'm forgetting characters, but it matters not. Lots of dopplegangers.