Also, there were a couple instances where it might have been better to do a return-to-hangar rather than standard jump-out. (But then I thought, perhaps you were trying to make it Retail-playable. Dunno if that's the case.)
Retail compatibility was indeed the goal.
So, why, particularly, is he waging a personal crusade against the GTVA and its citizens, and why in the heck are the officers and crew of the Altair Fleet enthusiastically following him in his mad campaign of genocide?
In case the spoiler tags aren't enough for you, this is one of those really, REALLY big spoilers. These are really big spoilers, as in spoilers to this campaign and another that I've not even started development on yet.
Bast is a pretty paradoxical character. For two years, he has watched the GTVA ignore the possibility of another shivan incursion. There has been no campaign to seal jump nodes, and proposals he has personally made the Security Council for the study of the potential of hybrid GTVA-shivan technology have been officially and repeatedly rejected. What Bast sees is a government failing to even acknowledge its most basic goal of defending its citizens. What Bast sees is the need for a demonstration.
His initial plan isn't to carve a path of destruction from Altair to the capitol, though. Initially, he attempts to sneak the Firestorm through lightly-trafficked areas to Delta Serpentis. Once there, they were to take control of the communication systems on the planet and attempt to send out a signal to 'wake up' any shivan units in GTVA space that may have gone into hiding after the destruction of the Lucifer in the Great War. He was then going to deploy the Galen to mop up these shivan forces as the demonstration that he thought the Alliance needed.
Unfortunately, the Firestorm broke down in Alpha Centauri, and the transport it was escorting was captured rather quickly, after abandoning the cruiser. Bast's subtle plan was doomed to be ruined by such x-factors as criminal activity and technical troubles, so he abandoned that. Utilizing the de facto communications blackout in Altair and his background in counter-intelligence, he convinced those in the Altair fleet that the Alliance was facing a widespread rebellion, the likes of which dwarfed even the Neo-Terran Front. Though this seems like quite a lie to swallow, intel coming into Altair has been getting filtered through Bast's office for some time now (recall that he cut the system off from civilian traffic, and most direct transmissions from GTVA Central Command never quite make it to Altair), so he had been finessing information to make this seem plausible to his subordinates for quite some time now.
(An important bit to note here is that a solid week passes between missions three and four, so the Firestorm has had time to be repaired and mobilized with the rest of the Altair fleet. I'm not sure I made the passage of time clear enough in the briefings.)
To call Bast's campaign one of genocide is to misunderstand his intention. He isn't out to kill off a particular group or even out to kill indiscriminately. Recall, he jammed communications in Aldebaran, and only attacked its fleet vessels when they attempted to intercept his fleet. He would have continued to act in such a manner, until, in Alpha Centauri, he was unable to establish a comprehensive jamming field, until after the Chicago and Phoenicia were able to get the word out about his attack of the blockade. At that point, the goal became speed (with the exception of approaching the Chicago slowly, rather than performing an intrasystem jump, allowing the station's crew to evacuate). Bast never goes out of his way to attack targets of opportunity, opting only to attack what stands directly between him and his objective, attempting to minimize casualties until the bitter end.
The big exception is the end of the final mission, if the battle goes lop-sided for the Phoenicia. Bast opts to bombard the capitol city, if he manages to jump into orbit. He is obviously unable to acheive his goal of capturing the central communication node on the planet, so he opts to destroy it and its backups, using bombardment of the city to mask his goal. At this point, his objective has become escaping GTVA space, as he has given his demonstration of hybrid technology in the worst way possible, and if the Alliance is unable to coordinate intersystem interception efforts, he will be able to get away without causing any more significant damage to the GTVA fleet. Even on the 'victory' track in the last mission, Bast seeks to escape, but the Galen is in no condition to attack the orbital blockade.
I'll leave it to you to figure out why he and his ship disappear in the Ross 128 system, though I will point out that it is more than just the Galen's combat systems that have been overhauled.
Were there any points that felt like they were more difficult than they should have been? Some bits are meant to be tougher than others, but I don't want trivial moments to be stupid-difficult (example: "Can't....scan....cargo....fast....enough.....AAAAAUGH!").
Addendum -- Woo. That's a big spoiler block....
