I know there is very big possibility you are all aware of this:
Anyone of you who played XCOM Apocalypse can remember moments when city police attacked UFOs side by side with you. I think it would be logical and nice to see military fighter jets joining the battle with you. Also, Phalanx weapons should be experimental and used only by Phalanx interceptors.
So, military jets of various countries should use normal, up to date weapons and equipment but Phalanx should use experimental, expensive, advanced weapons.
I think its not realistic that such organization (Phalanx) is using standard weapons and equipment. They should use most advanced weapons Earth has.
Another thing that would be logical are ufos flying in formation. Something like: after successful interceptions early in the game UFOs are starting to fly in formations.
Supply ships should be guarded by at least 2 fighters and UFO speed should not be constant (just like in ufo: enemy unknown).
To compensate this (in gameplay) military fighter jets are stepping in. It should be possible to coordinate attack with them.
I know people are giving you suggestions that you heard before, that you all were thinking about, I know its lots of work but hey, I love this game and I just wanna see it better and better with each new version