Personally, I don't think Smash Bros on 3DS is the worst idea. However, it's also not the smartest move. I can definitely get used to playing Smash Bros on the go! Though, no one can deny that it will affect the Wii U in a negative way. I already see some people on these forums saying that they will get the 3DS version of the game, with no mention of purchasing the Wii U version (or at least considering getting a Wii U for that version). That says quite a bit already. The fact that Super Smash Bros is also for the 3DS discourages people from buying a Wii U, since they already know the game is on a console that's cheaper and more affordable. I don't want any hate, but this is quite true. And trust me, I'm a huge Ninty fan that would love to see Nintendo succeed both ways :D
