Finally able to get at this again, but short on time, so here it is:
I would have liked a turn-based system better for all the players who cannot or do not want to handle the stress of quick decision making in an essentially turn-based game. Personally, I am fine with the X1 system.
As for effects, you should always set your goal to making systems as elegant as possible, i.e. easy to learn, good to use all over the game in certain situations and an option to consider all around. Thinking about the clouds, I feel you should go the step further and allow UFOs and later planes to generate their own clouds, and also to develop weapons that are immune (or at least resistant) to the cloud cover mechanism. This could lead to a nice X-Division style arms race between you and the Xenos. And the same should apply to everything you put into the air combat system. Have autoturrets on ships? Cool, let's also be able to drop them on hovering platforms in style the style of air mines.
The enemy behaviour system is giving me headaches: Having the enemy dynamically flee can lead to frustration on the player's side, so you have to be careful what to bring into there.
Finally: make pilots separate from planes! They could lose some XP when transitioning to a newer model, so your interesting decision would be preserved. You could also add simulators that could mitigate that to some extent.