Confirmed both editions of the game will have the very same characters.
Super Smash Bros: The Difference Between Wii U & 3DS Versions - NowGamer
Now to what can be seen as some unfortunate news.
Brawl Stages May Not Return for the Next Smash Bros. - Gamnesia
"If there was a character you couldn’t play on Wii U but you could play on 3DS, or vice versa, that’s rough for consumers. So we want players to be able to have the same character experiences on both devices."
Super Smash Bros: The Difference Between Wii U & 3DS Versions - NowGamer
Now to what can be seen as some unfortunate news.
Brawl Stages May Not Return for the Next Smash Bros. - Gamnesia