Well, I played through it. Liked the changes, for the most part. Eve of Destruction was a lot more intense.
I approve of what you did with Field of Battle. It never made any sense that there were just four wings of fighters sitting around in an asteroid field with no support and nothing to do.
Was it Small Deadly Space or Avenging Angels that had the big new cruiser fight? That worked pretty well. I'm not super sold on having corvettes in FS1; given the Morana's size, I think you could get away with calling it a heavy cruiser.
Loop missions were good, if a bit difficult. The one with the nebula in particular gave me a bit of trouble; I'd recommend maybe giving the player a hotkey to highlight the patrolling wings. The first one, though, where you're basically just observing the Shivans the whole time, was fantastic, with the only caveat being that it was a pain to keep track of all the cargo containers I needed to scan. The third was good too -- hard, but in the standard "you might need to play it a couple times to get the hang of it" way.
I think that's about it...