I liked the three 'run away' missions.
In mission 4 there are 3 battles where you can rack up a lot of kills but you have to shoot fast and true because there are time limits (New York) or the friendly NPCs kill the enemies fairly quickly and so you don't get many if you are too slow (Magellan).
In mission 7 you get several chances for battleship kills but you have to hit fast and hard to decrease the chance that a friendly NPC will steal the kill. Also, the 'Destroy the Rheinland Fleet' scene in Tau-29 (?) is one of the best battles overall because there is a nice menu of targets to choose from - fighters, gunboats, capital ships - and you can get yourself killed easily if you don't watch where you are flying.
Mission 13 I liked because it is challenging but fair; as in all Nomad battles in the campaign you can always replenish your shield batteries by shooting a couple of Interceptors and then go back to whatever you were doing (important if you fly a light fighter because the weak shield must be supplemented with batteries and 12 batts don't last long). Also, there is more than one viable approach for taking out the stationary targets and they are all fun. You can park your ship in a secluded spot near the target and fire away until it blows up (if you have a class 5 shield or better then you can also pop mines at it while sitting there), thruster on hair trigger so that you can speed away if you get discovered by a wing of fighters. Or you can make regular strafing runs and drop a mine when you break off. And the generators at the Nomad city are so big that you can play tag with the Interceptors chasing you by flying circles around a generator, all the time strafing it with guns and dropping mines at it.
Another nice skirmish is the return from the Nomad Lair in mission 12. The gunboats do not drop shield batteries so you have to make economic use of the Interceptors.
The only mission I didn't like was the one in Alaska (mission 11). After destroying the satellite you basically tag along and try to stay alive, but there is no real objective or purpose. The tactical situation is unclear - lots of hard enemies pop out of nowhere and are all around you. There are also a couple of script traps (where the game stops your ship's engine so that the Nomads behind you can catch up with you, things like that) and of course the Osiris is parked in a manner that allows the other battleship to fire straight into the docking bay ...