To my understanding smaller numbers where the main culprit in this process. Most missions actually drew only a small percentage of the players online. That wasn't really a big thing when a side could muster 100 players total, but when it's down to 20 players you won't get the necessary minimum number of participants to make most missions viable. When only 2 players show up for a basegrab or a fightersweep, you might as well just take off individually.
Smaller overall numbers also led to the decline of the big, multi wing squadrons of old, which made up the core of most large missions.
Bomber missions also got really hurt when the central strats where split up. It makes no much sense to conduct bomber raids on dispersed targets that a single player already can level all by himself.
Remember we once even had B-29 missions? (No idea how I could get the 'kill 4 B-29 in a sortie' these days'
)
And like so often, once a tradition is broken it's difficult to get it going again. The great mission leaders have mostly left us, and many players have never witnessed the constant stream of "MISSION UP!" on country channel. Which is a pity - I'm convinced missions where massively helpful to retain and train new players. These days, they are mostly on their own...