None of the other non-cosmetic mods are compatible out of the box. They might break your game right away, or you might realise you are playing a completely broken game after 10 hours. That said, good content is this:
Xenophobia. With the additions of AND_Great.
I think i have a fixed XNT version lying on my pc.
There is the X-Pansion pack, but i wouldnt recommend it. Stability wise.
All of aajs´s content. XMC.
Axiomatic s content, but its mostly geographical.
There is also Armored assault, and the Dreadnaught mod, which might or might not work.
Looking through the mod box in Xenonauts is mostly like walking through a broken toy factory. Nothing works, but everything is really interesting in its own right. If you just wanna look install whatever you see and then look what it does with your game, just dont expect a proper game afterwards.
X-Division and the XNT version on my pc are propably the only slightly bigger mods that is geared towards the convenience of the player. Given a proper installation everything just works.