Rule #1: NO. SUBSPACE. GARBAGE.
Honestly? Abominations that look like they belong in their own dang series? Way to shaft other Nintendo enemy characters that could have been. Is it really too much to ask for the biggest Nintendo villains around (Bowser, Ganondorf, Medusa, King K. Rool, and other enemy forces from different series, Space Pirates from Metroid, etc etc....Eh, Bowser may turn good at some point later into it) to come together to bring the world down using all their resources without all that made-up Tabuu junk and stuff getting in the way? If anything, Master Hand and Crazy Hand should be the only Smash-exclusive elements to it.
Alright, here's how the villain hierarchy could be:
As it first unfolds, we'd first witness the likes of Bowser and his Koopa Troop milling about and causing trouble all over. And sometime later, we'd see him teaming up with King K. Rool. The two of them would merge their Koopa Troop and Kremling Krew into one army and make for kick-arse double trouble all over the Nintendo World right there.
As it goes on further, we'd see that Space Pirates under Ridley and Dark Samus are getting in everyone's way, even going after Bowser and K. Rool and also using their Phazon to corrupt everything around. And sometime, the Koopalings would make their appearance, but following Bowser Jr. and going on as a league of their own away from Bowser.
And then of course, there would be Ganondorf. He'd have his own army, but maybe he'd follow along with Medusa and her Underworld Army.
Other leagues of their own would include Wario and Waluigi, prancing around on their own and ambushing any heroes they may encounter. And King Dedede too, whatever stuff he may be up to on his own.
May expand upon this later...