Fantastic Four director Tim Story told Latino Review this weekend that Doom will indeed be back for the sequel:
Before I hopped on my ride to the airport back to NYC I asked him when does shooting start, Story replies, “August 1st up in Vancouver” And finally I asked Story that towards the end of the film it left wide open that Doom will be back, so will he? “Yes that I can tell you. He will be back in full DOOM, not like we had him in the first film.”
He also talked a bit more about Kerry Washington’s character, Alicia Masters, which you can read at the link above.