Why not set this up as the PUG tournament that was run a few years back?
Once theres a pool of 50 or so willing players, all of the players are randomized into 6 or 7 separate teams, and then go from there?
That way, every team has a good chance of winning, and its not just one or two teams going undefeated and everyone else having nothing but losses?
More competitive = more fun
Another idea which is similar to this one would be to get the same 50 player pool, and then choose 5 captains, 5 permanent commanders, and then allow the captains to choose their own their squads. Spearwolf or some other neutral, trustworthy player, could randomly choose the order in which the captains choose their teams. Of course, there is only 1 pick at a time until all players have been chosen.
Thinking into this, I realize that there might be a problem with getting all of the team captains to get online together at the same time, which would be necessary for this "drafting" pug idea to work. Also, it would be smart for the captains to choose at least one player aside from their designated commander, who can also command decently well just in case the designated comm can't or doesn't show up.
Anyways, this is a fantastic idea that you've come up with spearwolf, I think its going to work out for sure. It seems like a lot of people are interested in some more competitive savage. Just remember, try to remain organized and be ready to make changes to the system when needed.