Well, UEF fighters and gunships rock hard. They're built for short-range, high-intensity operations in a single system, so while they're not as cheap or maintainable as GTVA ships, they can really do some damage.
Plus their supply lines are much shorter and their infrastructure a bit more centralized and built up.
It's a decent strategic balance. (Tactically, their torpedoes are pretty formidable too.)
All that said, the war at the beginning of War in Heaven has only lasted eighteen months - it's an incredibly high-intensity conflict compared to something like WWII, though the number of people involved is much smaller. Billions of lives and entire planets are riding on the shoulders of relatively few pilots and crew on both side, and as the for the physical intensity, a bomber pilot might expect to expend more raw destructive force in one sortie than all of World War II put together (maybe; I haven't done the ballpark figures. But it sure sounds cool.)