One of the cool things I liked in FS2 that FS1 didn't have was explicit squadrons. Also the fact that in FS1 an Admiral was talking directly to you about doing the third watch is kinda silly. Someone has probably already thought of this, but how about changing FS1 a bit to the more realistic style of FS2. Kinda like a FS1:R, but not as dramatic a change as in ST:R.
Say for instance in Eve of Destruction, you get assigned to some squadron (to be named later), commanded by Lt. Harbison. Instead of Admiral Wolf briefing you, Lt. Harbison does. "Hey, you're doing the third watch today. Since this is your first assignment, I'll be there with you." Or something like that.
When you get to the McCarthy mission, since you are such a great pilot, you get to join a brand new squadron, the Suicide Kings! You play with them for a few missions before joining another squad. After a while, you join a recon squad for Playing Judas (maybe you get kicked out because you did something "wrong" in that mission, like trying to fly into the Lucifer's docking bay like command said). Near the end, you join (or even lead!) the Hammerheads on the Bastion and take down the Lucifer.
Of course, this is a departure from FS1, so that is why I would tag it FS1:R. Non-canon, but still cool. It wouldn't be that difficult to change the mission briefings without changing the storyline. Those node inconsistencies (and other small bugs) can be ironed out too. What do you think? Oh, and if someone has done this, please point me to them.