Well, I'd like to see some kind of "Legion of Doom" trying to conquer the Universes.
I know it sounds cliche, but if they play the card right it could turn into something really awesome.
I can imagine Bowser, Ganondorf, Mother Brain[with Ridley by her side], Porky, K. Rool, Andross[with Wolf], the boss of a possible evil team from Pokémon, Medusa, Ashnard[Fire Emblem] etc. sitting together and plotting.
They'd send their minions and bosses to fight the heroes, but failing until they run out of staff and go fight by themselves.
Maybe even Tabuu[2.0] could appear in the end as the master mind behind everything. IDK
I know it sounds like the plot of SE, but the "Legion" in Brawl wasn't really a BIG conspiracy like I thought it would be. It was 4 guys taking orders from a giant puppet hand...