Awesome job! Only one serious problem I encountered was with red alert missions - as already mentioned, if alpha 2 and 4 died in previous mission, apart from command chating instead of alpha two, taking down aeolus cruiser is ridiculous.
Same stuff happened during gas miner mission - if alpha 1 is down, the command takes over his chat. Maybe some indestrucibility flag for him? ^^
Apart from mentioned minor issues - great campaign!