One of the things I think would've been cool is if President Luthor had appointed Norman Osborn as head of SHIELD/HAMMER. In retrospect I wish DC had been thinking more along the Dark Reign lines as fully as Marvel did when Lex became president.
Also, Amanda Waller knocking heads with Luke Cage on a Thunderbolts/Suicide Squad team would be interesting.
A Black Panther-Vixen romance. Or Catman (Secret Six version) v. Black Panther would be pretty cool. As would a Bronze Tiger v. Panther match up.
Bullseye v. Deadshot would be nice. Deathstroke v. Elektra or Lady Shiva v. Elektra could be awesome.
Merging the Doom Patrol with the X-Men probably wouldn't be too hard to do.