2nd - on the last mission, Prince Charles shows up to fight you, but instead he goes after your team mates, and in 99% of the time, he starts to dive trying to flee from everyone, which causes him to crash and die softlocking the player, i would suggest changing his IA so he becomes more manouverable and is hardcoded on chasing the player instead of the unkillable NPCs, and your team mates to not attack him and attack the royal guard instead.
I would also suggest spawning more royal guards so to keep the NPCs busy and spawn the prince way higher, if he could keep to a certain distance away from the floor, that's a bonus.

1st - on mission 2, an ACE Squadron that could be very much a boss fight is given plot armor fsr, can you make them just have a very large health pool ? so if i am a maniac and decide to kill them myslef instead of let them die offscreen
The basic missiles seem to do around 500DMG, special AA Missiles can cause up to 2000 DMG, at least that's what the game says

since you are on the business of fixing missions, i have two problems with this campaign:

EXTRA:
Here's another small fix for mission 6: in the .msn file, change the following lines
from:
8_Trigger_typeID = 0
8_Trigger_ScriptID = 11
to
8_Trigger_typeID = 1
8_Trigger_ScriptID = 4

this will prevent the mission from abruptly clearing before the final wave is destroyed,
you may ignore this if you're fine with how mission 6 goes, just sharing some tips.