This has certainly been touched upon previously in this thread, but man does this game suffer from some poor pacing. It's an incredible game otherwise, but often it feels like the developers are actively working against the mechanics which primarily make the game more satisfying.
It's been a while since I played the first one, but I don't really recall there being so many forced time-sensitive missions being forced down your throat one after another. It's so frustrating to clear one mission with a plan formed in your head on how to improve the squad and equipment, only to have the development metagame being cut off by some fucking guerrilla ops mission or something. It really hampers the enjoyment I get out of what I think is one of the constitutional mechanics in this game.
Of course, there's the possibility to skip a mission, but then the game presents you with a message along the lines of "IF YOU DO NOT DO THIS THERE WILL BE CONSEQUENCES". Which kind of forces me to do them as I don't want my campaign to fail.
These abrupt ad hoc -missions also really fuck with you when you're trying to do an actual mission. Sometimes you're all set and ready to go, and the game hits you in the face with a Retaliation Strike or something when you're traversing to the mission location. Jesus!
While the combat gameplay is good, much of the enjoyment in it comes from testing upgraded equipment and soldier abilities in the field, as well as fighting new enemies (which are extremely well-designed and very interesting). Doing these trivial missions removes the excitement from the combat as you already know you're just going to do the same VIP extraction you've done like 20 times before.
It's odd how this problem wasn't picked up during testing.