By endurance, you mean "more free time than the other team has." Playing a video game doesn't take endurance, it takes time. If people start slipping because they aren't in the game after 5 rounds, then its because the game is no longer any fun, and that defeats the whole purpose.
No way I'm playing more than three rounds.
If there was a Home/Away system, where Visitors always got Aliens first (to make up for home server advantage), the current best-of-three would suffice, because every clan would have a great Away record and a crappy Home record (and your road average would show how good you are at Aliens and your homefield average would show if you suck at Human or not). It sucks to lose on your own server, but it would be consistent. For any match to be declared valid, you have to play two matches against that clan, one Home and one Away (three times as Aliens and three as Humans). If you can win Home as well as Away, you are better than them. If you both win on the road, you're equally good at Aliens (and equally sucky at Humans). If you both win at home, you're equally good at playing on your own server.
Match 1: 3 games, ClanY server (map stays same)
Visitor (ClanX) Aliens - Home (ClanY) Humans
Visitor (ClanX) Humans - Home (ClanY) Aliens
Visitor (ClanX) Aliens - Home (ClanY) Humans
Match2: 3 games, ClanX server (same map)
Y=A; X=H
Y=H; X=A
Y=A; X=H
Record of two matches played on two servers is used to decide which clan is better; one match on one server insufficient. If they don't have a server, they have to be the Home team on your server, and start as Humans, for the second match (they don't get any real admin status, though).
What map, rotation (if any), how many players per team?