I guess they could continue the whole bio-terrorism storyline with another antagonist. I mean they made it clear in Resident Evil 5, that viruses, and bio-weapons were being sold on the black market to terrorists.
Maybe Resident Evil 6 can go back to what Resident Evil 2 did. Have a virus infect a US city, and have the BSAA called in to investigate.
They could also explore Ada's story a little more, and let us learn about the organization she was working with behind Wesker's back.