I don't think it would be unfair to Wii U owners since alternate colors would probably still have different colors, hairstyles and maybe even faces.
It's like Villager, you have gender options, hair options, eye options, etc. So if you want a specific one it's there.
This whole option is just more of a bonus for those people who played the games and have a specific attachment to the characters they used when playing. Like, if I got hyped about Robin because of the Robin I used in the game, it would sure be nice to have her in the game. Someone who didn't play the game probably wouldn't care because via alternate costumes they're still getting the variety.
And if they do care then they're probably at the point of liking the character enough that they'd probably play the actual game itself, and I can hardly imagine Nintendo seeing that as a bad thing.
Personally, I'm hoping more and more that it is an option, particularly since it seems streetpass hats may be loaded into smash for the miis. It'd be a bit disappointing if they gave all these options to the miis but didn't try to do so for villager or robin. (Granted, Villager is a tougher enterprise due to clothes also playing a role. I can hardly imagine every attire having a smash bros HD counterpart ... maybe it would just change the head but keep the attires from the color options.)