I didn't feel like that. Prophecy at last didn't have the "Two pilots against the galaxy" thing that was a staple of the series since its inception.
I had a very different read as well, especially in Special Ops where the Federation really starts throwing its weight into the Nephilem war. At the time, that mission where you're sent to rescue two Murphy destroyers and a Plunkett cruiser was THE largest space battle I had ever seen simulated to that point. There were legitimately great missions, and your wingmen weren't useless. You were simply fighting overwhelming numbers.
In Prophecy, the point was that Midway was the first major Confederation response to a new genocidal alien race. The race was to shutdown the wormhole so a proper response could be prepared.
On a lore note, the Wing Commander Armada manual, the last bit of actual canon WC lore, stated the Confederacy/Kilrathi alliance eventually won the war against the bugs, but it was a grinding slaughter fest for most of it.