Overall, I enjoyed War #4 (the only war I've participated in) and the only real complaint I have about how it was run was, as many have mentioned, the system where not losing was rewarded more than winning. A team that completely fails the first few rounds, and then has to play less teams, will do better than a team who consistently excels every round.
For example, team Death won war #4, with a W/L record of 29-21, or 58%. Team time, who had five more wins, and the same number of losses, made it to 3rd/4th. Team light, who had a 21-20 record, or barely 50%, got 2nd place, though their win percentage would put them at 6th. Team earth had a 32-20 record, or eleven more wins than team light and the same number of losses and got 3rd/4th place. Based strictly on win percentage, team time had the highest, with 61.8%, followed by earth at 61.5%. And while I am definitely biased, having been on team time, I felt those were the two best teams this war. I think team earth was the best team this war, and team time was runner-up, but the war results don't show that.
The highest weight went to the games near the end of war, which are also the games that take the least skill to prepare for, since vaults are almost completely known and only one or two decks can be fielded. Buliding a deck that can win no matter what the opponent brings takes far more skill than 'oh look, we each have one deck left, I guess we'll play that, and oh, we know team A will win before we start'. One suggestion I had made was to have teams eliminated before it gets that far, so that instead of the elimination threshold being 30 cards, it is higher, say 100 cards. (and that might require larger starting vaults) This prevents the 'we both know what the other guy is using so it's predetermined' problem that reduced the last rounds to pure luck on who matched up against who. There is always going to be an element of luck, of course, and this is fine. The scoring system, however, shouldn't magnify this to the degree that happened this war.
The other complaint isn't about how war was organized, but how certain teams gave up earlier on by suiciding before it was necessary. Of course, again, I'm biased because I was on team time, but it just happened that almost all of the (unnecessary, as opposed to strategic) suicides were in matches against death and entropy, two of the top 4 teams (earth and time were the other two), so it hurt us a lot more, and so annoyed me more than it might have some other teams. If you're going to sign up for something long term like war, at least stick it out; it lessens the fun for those who remain. If you really don't want to play anymore, and I know it happens, maybe war wasn't as fun as you thought it would be, rather than suiciding, why not have some of those who didn't make the initial bidding take your places instead and give them a shot? That way, those guys get a chance to play, you guys don't have to play anymore, and those who stay don't have the experience spoiled by those who don't want to play anymore. /end 2 cents