The Doom/Kang War
The villain side of the Secret Wars had some pretty heavy hitters, people who should, even on their own have made a challenge for an entire collective of heroes. I'm not talking about Galactus--he's so over-the-top he's more a plot device than a character. I'm talking about Doctor Doom, Kang, and Ultron. Of those three, Ultron seems a little two-dimensional to be interesting, but the idea of Doom and Kang both stuck on the same mudball of a planet is too good to pass up. Neither of them are really the kind to play second violin, so I'm thinking that in the aftermath of the Secret Wars both men head off in different directions. Doom creates New Latveria, populated largely by Doombots, a handful of home-grown supervillains like Titania, and a few stray humans who for whatever reason can't or won't live in Denver. Kang on the other hand is all about raising an army to conquer whatever he can, and I see him heading out into the Battleworld to recruit aliens also stranded on the Battleworld.
So what you have is a sort of Cold War between the two. Kang launches the odd clandestine foray into New Latveria, while Doom sabotages Kang's attempts to coalesce enough troops to seize control. Both of them could subtly direct fledgling heroes against the other, pawns in the Great Game.
Of course, eventually it'll go from Cold to Hot, and you know Denver will be in the middle...