I know it's still in Alpha, and I don't know what will be changed, but I hope the overall quality of the textures and animations on the Battlescape is improved. Things are just much less crisp and defined than Xenonauts 1, which I thought looked excellent. Also, the way the edges of foliage interact with fog of war is very unappealing and results in a lot of jagged edges.
I understand the need to switch to a new game engine, but I really liked the 2D look, and I think it's going to take a lot of work to achieve the same level of fidelity in 3D (look at an old 2D game like Desperadoes or Robin Hood: Legend of Sherwood compared to 3D games even years later...). I hope there's still a lot to be done, and that it will look great! It would be a shame if the sequel continued to look inferior to the original.
Note: I'm not talking about the obvious placeholder art.