I gotta be honest... I thought a GTI victory would have been "less worse" than an NTF one. In fact, a GTI victory might even have been better for the GTVA, as most of the technologies that they were experimenting with in the canon were effectively lost. If they hadn't been lost, would the GTVA have been better equipped to produce better beam weaponary and other weapons based on Shivan tech? I think they would have.
Also, the NTF were insanely destructive in comparison (in my opinion). My justification of this is that the Knossos would have eventually been found and activated one way or another and the Shivans would have returned, therefore making the events of FS2 inevitable bar the NTF factor. If the Trinity had not activated Knossos and triggered the second Shivan incursion, the GTVA might have had more time to create more warships or implement better technology. Could they in fact have built a second or even a third Colossus? Would there have been more destroyers with better armanents available? Also, if there hadn't been the inconvenient distraction of the NTF, could more resources have been deployed to Gamma Draconis to stop or delay the Shivans, which might have allowed more time to evacuate Capella and saved a lot more lives?