In the latter part of 2000, I was working on a TC plug for EV called "Great War", which dealed with this war. I had all of these problems as well, here's how I solved them.
The Aliens (which I renamed "Kurvaians", using the Polish word for "whore" and adding "ians" to give them some identity), lived north of THX-1388 in a little over a half a dozen planets. These were very far away, in another part of the galaxy, but a huge alien station harnessed space power to create a hyperlink between the Alien worlds and the Human worlds.
Had my pluging been carried to full term, the human missions would have destroyed this station, cutting off the link from the ALien homeworlds to the human worlds, leaving only a small ammount of alien ships to be dealt with. The Confeds still used Mantas, even though Patrol Craft existed. I imagine that any campaign against an Alien ship would invole flooding it with dozens, perhaps hundreds of fighters, both Mantas and Patrol Craft (Patrol Craft have better shields, but nothing beats the effect of hundreds of speedy Mantas overwhenlming a target, even if it is with lasers). Eventually, the aliens would become "extinct" in our area.
Of course, I made all of that up for a third party plugin, and it is probably not what the creators of EV were thinking. More likely, they imagined the Aliens as nomands with no homeworld, and by destroying their fleets we destroyed all they lived in, casuing them to become extinct for real.
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