I think the 6th Fleet wasn't exactly trusted by GTVA command even before the rebellion, so they got lesser equipment. Also, it would appear the Herc II, Myrmidon, and Perseus are relatively new, less then three years old. The defecting NTF had minimal numbers of these to begin with, because deployment had begun only a few months before the rebellion, and what they did have has seen 18 months of combat, during which it has been damaged/destroyed/generally messed up. Also probably the NTF has very few spare parts left after 18 months of combat ops for those ships, so they aren't used much for fear they'll break and be unfixable.
There's also the matter that the NTF Rebellion actually helped the GTVA deploy the newer equipment more widely, in a sense, because they didn't have to deploy it to the fleets that had defected to the NTF. In all likelyhood, you wouldn't have had quite so much of the advanced hardware at your disposal in FS2 had the NTF Rebellion not occurred.
Of course, without the NTF Rebellion, there would be no FS2, because the NTF wouldn't exsist, and the Shivans would still be on the other side of a shut-down Knossos...