I personally prefer the system where you place your modules in your inventory (the initial system).
The "toggle button" for armor and other modules is an interesting idea too, but I prefer "seeing" the modules in my inventory as it feels more "real"
Thumbs up on abduction missions not ending straight away, and having the tubes teleporting away. (i assume i can kill the aliens even after X turns when the tubes are gone)
I do prefer funding to rely on panic level. maybe instead of becoming unrelated to panic level, panic could simply carry a bit less weight in determining the funding level.