I would expect the next LCG from FFG to be based on an existing property, and one tht FFG already has the rights to. I'm basing this on the one big cost of a start-up card game artwork. When a Core Set comes out, it requires a large card pool, usually made up of at least 160 new cards. Which means 160 new pieces of art. And that can be a huge investment. If they can base it off of something they already own, they can reuse the artwork. Which means 40K or Twilight Imperium, or possibly even Cosmic Encounter are strong candidates.
Myself, I'd love to see them acquire the rights to Shadowrun as a LCG. That would totally rock. And bring Shadowar into a UFS LCG. They spent the time designing the property, might as well get their the money's worth.
Hopefully it won't be Mutant Chronicles. THe minis game was impressive, but how many people besides me had heard of the property before.
One last note. AS someone already mentioned, FFG has already acquired the rights to the AH Dune game, but can't publish it as Dune, as the Frank Herbert estate wouldn't resell the license. But they have the rules and the "engine," as it were, and are going to rerelase the game my guess is as a reinvention of their old Hex game, Thunders Edge.