I'd ditch the unwieldy TU system for an action point one ALA Fallout (especially Tactics) or Divinity Original Sins personally. Action points work because you can make every single one feel meaningful when you have 10, maybe 12-13 maximum, thus design and balance the game accordingly. As I said somewhere else, when you have 56 or 73 or 81 TUs it becomes needlessly complex if you ask me, and memorizing the TU cost of every single menial action gets boring fast.
I'd also make the AI less cheaty somehow. People can complain about the pod system in the XCOM games all day long, but Xenonauts had even more bullshit moments such as aliens walking in range of your soldiers and instantly gibbing one, or even a few times snipe you from outside visual range.
Also more battlefield options. Now, I'll admit I never finished Xenonauts, so it may be that the lategame gives you loads of nifty toys, but from what I played you didn't get that much new stuff, mostly stat upgrades as you went along the techtree and soldiers got incremental skill increases. Compared to XCOM2, where you get loads of soldier abilities as well as ammo types, grenade types, psychic powers, support items and heavy weapons, it was sorely lacking. Taking 50% shots en masse is only fun for so long.
And an art style that doesn't look bland. I'm aware that they don't have Firaxis's ressources and can't make everything flashy, but Xenonauts was painfully boring to look at. Technical limtations are one thing, but a more inspired art direction would do the sequel some good. No need to go crazy, just inject something interesting in the package.
I do like that XCOM doesn't occupy all the market in its genre, and that a game that tries to emulate ye olde ones can prosper alongside Firaxis's re-imagining. The fanbases of the two games are also surprisingly friendly towards each other, albeit I assume it's partly because many players just enjoy both franchises.