Seems pretty obvious to me. Custom moves. Think about it.
With the WiiU, everybody would need to customize their characters before games are played in each system they go to. This is a major inconvenience that'll just make things last longer, and they might be banned anyways.
But the 3DS is bring your own DS. Your customizations will already be saved on it. No time, just pick it up and go. If the WiiU version doesn't have custom moves approved for tournaments or the like, making them allowed for the 3DS will completely change the game. Everybody playing 3DS competitively will have full customization support, and you need to adapt on the fly to your opponents customizations, putting more strategy into the pregame than ever before.
With the WiiU, everybody would need to customize their characters before games are played in each system they go to. This is a major inconvenience that'll just make things last longer, and they might be banned anyways.
But the 3DS is bring your own DS. Your customizations will already be saved on it. No time, just pick it up and go. If the WiiU version doesn't have custom moves approved for tournaments or the like, making them allowed for the 3DS will completely change the game. Everybody playing 3DS competitively will have full customization support, and you need to adapt on the fly to your opponents customizations, putting more strategy into the pregame than ever before.