Over on the Goldhawk Forums, Xenonauts project lead Chris England is raising everybody's hopes for Xenonauts 2. His language is tentative but promising. "We're still evaluating the possibility," he says, "But I'd say the chances of us making Xenonauts 2 as our next game are better than even."
Apparently community feedback has helped to convince the team to make a sequel, but it's still possible that they might go in a different direction. The codebase they've been working on in the time since releasing Xenonauts would work for any "squad-based tactics game" they want, so it's possible their next game will tell a new story in the same genre.
However, it does look like they've been doing a lot of thinking about Xenonauts, for instance testing a 3D art style, redesigning the aliens from the first game, and considering whether they're able to create a new strategy layer. England says that at this stage the team is "actively designing and prototyping" Xenonauts 2, but it'll probably be one or two months until we know for sure whether they'll commit to it as their next project.