More bugs. The bane of any FREDder
1) If the Alexander succeeds in escaping you shouldn't really get a commendation for protecting the Fulligan. It would probably look better if that message only appears if the Alexander was disabled.
2) If you're sneaky you can get Beta Wings bombers to stick around to help you out. If Beta have been told to protect the Fulligan then those orders have a priority of 100% compared to the maximum of 89% for the ai-warpout SEXP. Use the departure cue in the ships editor instead.
3) It is possible to destroy the Alexander instead of disabling it. Nice try switching it to friendly and SEXPing the ships to stop but if you load up everyone with Tornados you can actually kill it before they kick in.
Add a SEXP to recall the player and a Debrief to berate the player suitably cause at the moment it completely breaks the mission.
4) After disabling the Alexander the damocles jumped in. Someone (I think it may possibly have been beta wings bombers) then proceeded to blow it up. At this point the mission broke again with the NTT Omega coming in to dock with a non existant cruiser and Striker talking to it too. If it was beta wing then fixing 2 will take care of the problem.
5) You should add some dialog to make it seem as though GTVA marines are fighting on board the Alexander because it isn't quite clear why the player shouldn't just blow it to hell.
6) While looking through the events I've noticed that in the reassign Gamma event Gamma are given ai-chase orders with respect to the Fulligan. Surely that should be ai-guard?
7) My main problem though is that the mission is still too hard. I tried and failed to take out the alexander 5 times using the forces at hand before I gave in and simply gave myself some stillettos to do the job with. You might want to consider hinting in the briefing that the bombers are armed with Stillettos so that the player is at least thinking of using them himself. You may also wish to be less subtle than that
One method I've used in the past is to suggest that the player (since he is the squadron leader) can choose between a bomber or fighter role. Even though the mission is unplayable in a bomber that would at least get the player thinking of taking down the Alexander himself and turning Beta into a second wing of fighters.
8) Keeping with things being too hard. I like what you did by checking the skill levels but I think you should bump it so that the differences are between missions played on hard, medium and easy rather than medium, easy and very easy. That 5 second change would probably make the mission much more playable.
Apart from that this is a pretty solid mission. I'm impressed by the trouble you've taken to anticipate mission breakage and counter it.