Missions, first and most importantly are suppose to be fun.... for everyone, friend and foe alike.
For me the only reason to run an NOE mission, is as a support to the main mission. Say your hitting a base, and while you knocked out the VH the enemy is spawning GVs in from another base. Shifting the battle to the other base would pose the same problem, and the defense is high enough that your going to need more than the 15 minutes it down to get things under control. You assign 5 or 6 guys to run an NOE to the other base to try and sneak it, all the while maintaining the battle you have going. Defenders have two battles IF they spot it...more fun for both sides... you relieve pressure at the main attack and force the defenders to work a new tactic...more fun for both again.
All other missions should be of some altitude. High alt bombers lift 15 minutes before fighter escort, will give you rondevous at high alt. Mid alt needs more fighter cover, so you need some fighters heavy for clean up, others lite for cover. Having a couple of buff groups hitting ord and SB just as a CV group launches an attack can be tough to time out but is really cool when it works.
When I was CO of a squad, squad night I felt it was my duty to make the night as entertaining as possible. The more fun the squad had the more guys would show up for the next one. Its all about having fun. You have to look at your missions from the other side too. You said you run a lot of NOE missions, and commented that the Knight probably hate them. If the Knights had been doing them to you, would it have been as much for you as running them? I think not. Plan your missions to have fun, COUNT on defense poping up and make it PART of your fun. If you hit a base with 20 guys and only a few defenders show have your guys back off the field, only shoot guys that come out of the ack. You have enough people to put a circle around the ack, let the defenders give it a go. More fun for them, and more challenge for your guys, so more fun for them too.
To many people believe that the object of the mission is the capture, but its really to create fun for as many people who want to join in it.