My apologies, I did not mean to be insulting.
Here are a bunch suggestions...
1) Get rid of unnecessary events.
'success pt2' and 'failure pt2' don't do anything, as far as I can tell.
Also, you have events (plural) that maybe handled with single events.
These things will help others to understanding what's supposed to be going on. (Sorry, but being a newbie-programmer, I still have that maxim going through my head: 'Make your code understandable!')
2) Your bonus objective should be more encompassing. For example, what happens if Omega 3 is destroyed before it can dock with a cargo container? Your bonus objective doesn't handle this possibility. Make a clause in your bonus allowing for the player to destroy both cargo containers if necessary, not just one.
3) Fix the deaths of Omega 1 and 2. This can be done by making a repeating event that repairs turrets 1, 2, 3 and 4 on the destroyer to full strength every second. OR you can change the entry angle and/or distance of the destroyer and/or the transports so that the destroyer can bring more cannons to bear on the targets, allowing for the transports to die quicker.
4) I think you may have seen this bug already, but here it is...
When you have Omega 3 take Cargo 1, you fail to make Cargo 2 vulnerable. Instead, the event makes both cargo pods invincible, making it impossible to fullfill the bonus objective. The opposite is true when Omega 3 takes Cargo 2. This is an easy problem to fix.
That's all I remember right now. But this should help make your mission run more smoothly.