A couple more thoughts.
I know grenade arcs are an incredible pain in the rear, but I find some of the current arcs unsatisfying. You can throw grenades over many tiles of intervening cover, such as over a building or over one of those jungle plant clumps on a tropical map. Such a throw means the arc would be very high at its highest point, which indeed the graphical preview confirms, but those arcs are well beyond what seems realistic. It just messes with my expectations as a player, on both sides. I was on the receiving side of a very surprising Wraith grenade on a jungle map, and I several times found my soldiers being able to make throws that intuitively felt impossible.
A height ceiling might be in order there - grenades are powerful in any case, and they probably work better if they're limited to paths that are somewhat realistic. Throwing grenades over walls or hedges is good, being able to throw them over wide buildings is too much. It's a grenade, not a mortar.
On the economy side, I'm getting the feeling that manufacturing is impossible to keep up with. There's a lot to manufacture and, having built a third Workshop at my main base (with adjacency bonus), I'm constantly behind. It's great that you have to pick priorities and can't build everything easily, but I am not sure if the balance is right. Even the basic Angel interceptor is buildable (unlike X1), and we have to build aircraft weapons as well. Early on we get access to Accelerated guns but building a full set of those is slow so more gets researched, and some time into a campaign I find myself very behind on manufacturing. I don't have a full set of the latest weapons for my team, I don't have Alenium missiles on all my planes, I can't even think about upgrades like Alenium Generators.
Perhaps that's intentional or I'm not playing right, but my intuition is that manufacturing is about 20% too slow - though I certainly love that it's overall tougher and requires more planning than X1.
Stunning aliens is weird, you can have a nearly-dead alien survive smoke inhalation and stun gun fire. I understand they have different health/stun pools but it would feel more intuitive if the stun pool also dropped as their health drop, to some extent. A badly wounded alien shouldn't be too difficult to stun.