Since this new F4 movie will be a reboot it seems likely they'll go back to Doom. Fox rebooted X-Men and went right back to Magneto as the villain so... Track record? I'd be more than happy to see a different villain, though.
I liked that the reboot of Spider-Man didn't go with Goblin but Lizard instead, seeing as how he was teased in two previous films. Even though we're getting Goblin in the second...eh.
Magneto didn't really emerge as the villain until the end of the movie. Shaw was the baddy in the reboot.