The GEFs are no more, they where either vanquished or assimilated by the GTVA.
Do you really think all those GEF fighters that you fought where flown by GEF pilots?
You could hardly be wronger. The Gefs have been supplied for 18 months by both the UEF and the Tevs, both trying to use them against the others. Some Gefs cells are working with the Tevs, some are working with the Feds, some are working for neither, either keeping a low profile or striking targets of opportunity on both sides, and some are probably just giving themselves as guns to hire. None of them are directly under the Tev or Fed orders, they're just a wild card they try to influence the best they can. We're talking about a vast, fractioned faction of which a
single cell nearly managed to capture a top-of-the-line Hatshepsut by itself.
EDIT : Also, I might add that given the sensible nature of the previously mentioned operation (if what happenned there was to be known, Steele could loose his rank or even be sentenced to death for high treason, conspiracy against Vasudans, for hiding critical intel and organizing a direct assault against critical Allied assets, this could even start a second T-V war if the Zods decided to take it bad), Steele couldn't afford to crew the Scimitars you see in that mission with SOC pilots, and I don't think he even has enough SOC at his disposal on the whole Sol theater for this. We're talking about dozens of fighters here. It's much easier, cheaper and safer to silence a few Gefs than your highly skilled fellow SOC pilots.
Every GEF Fenris or Leviathan has most likely been downed by the time the war with GTVA begun, same goes for anything big enough to be tracked down and bombed.
The Tevs managed to hide a Titan-class carrier for a good half of WiH. This is a much bigger target to hide, especially for people who don't know the battlefield that well. I don't see why would the Gefs have any problem to hide a flotilla of cruisers or larger, since they know the terrain, and most of the UEF sensor infrastructure has been down for a while anyway.