Uhh.... the GTA lost almost 40-50 full squadrons worth of pilots?
Doesn't say anything about them being isolated, just without supplies for the time being, the GTA forces, being so knackered, aren't really in a position to take advantage of that.
It also doesn't mention any timelines for the system.
It also doesn't mention how many cruisers and if any destroyers were lost in the offensive.
Anyway;
Joint projects (afaik);
Thoth.
Uly.
Avenger (in the end).
Shields.
Interceptor.
dunno 'bout the rest ;p
Seth > Valk > Apollo > Anubis (though, I saw this from never having flown an Anubis).
Leviathan > Aten=Fenris
Typhon > Orion.
Alpha 1 > *
I don't think we should take the story as what it would have been if it wasn't a game though, Alpha One gets glorified quite a lot by briefings and debriefings even for minor missions.