I still think it would have been a better marketing decision to make the rosters different on each version similar to what they did with the stage lists and the game modes as well. (Yet, I see hardly anyone complaining about that.)
After all, Nintendo has done similar the Pokemon series for years now. Just make it where you get a few exclusive characters on the 3Ds and the Wii U then throw in some cross platform trading and suddenly they'd be rolling in cash because there would be a big incentive to buy both versions. Suddenly people that only own a 3Ds will think about getting a Wii U and vice versa.
Though many would consider that very anti-consumer for Nintendo, need I point out this is also the same company that's releasing the New 3Ds months later for the US which would have been perfect for Smash Bros. So now if you never had a 3Ds before Smash comes out, you either have to wait until the New 3Ds hits the shelves to get the game or buy both and sell your old 3Ds. So in all honesty, I don't see a reason they couldn't stoop to making characters exclusive in Smash.
Plus, the fact that the ice climbers were cut from the Wii U when they already had a working version means that the time they spent creating that character was wasted. Time they could have spent developing another character that didn't get in.