I'm all for a sequel/remake.
What I would want (and granted mods definitely helped in this area) are more maps/variation and a slower but larger progression in terms of adapting technologies. For example maybe be able to make modifications to existing aircraft rather than purely have to build new craft, at least in the early stages. I would like to feel like I'm still cobbling together alien technology for human purposes.
Maybe more options with land vehicles as well: Troop transport, mobile medical station, sensors/IR, calling in tactical strikes? Just throwing ideas out.
I love Xenonauts and I trust you'd do something great. Glad to hear you're considering another iteration on the game!