My war experience has been soured for several reasons. Many of them stem from losing our master as the event began, causing members of our team to step up leadership roles.
There are more broad, general things I feel could be improved; however.
The initial stages of war are where the event really shines. Everyone has a chance to participate, and deck creativity plays a huge role in team's success. Unfortunately, the penalties for failing are very minuscule at this point. Deck creativity and the element of surprise eventually goes away when the stakes really matter.
Dwindling vaults cause a situation where it becomes a pain in the ass from an administrative standpoint. Juggling these vaults and taking penalties really takes a lot of fun out of things for people. Dwindling vaults also exponentially decreases creativity and increases predictability. This further penalizes elements with major flaws in the way that these flaws are more easily exposed in the deeper rounds.
Why even limit vaults in the first place? The rules restrict in a way that keeps decks true to their elements already, and allowing teams to shape their decks according to opponents would make for more interesting matches. There are other ways to keep track of standings, without making them entirely dependent upon vault sizes.
I would also propose that war be shortened. To have the event span months is much too long. In time, it becomes an endurance contest based off of who most successfully avoided silly penalties, who was blessed by RNG in matchups, and who was seen as "strong" enough to have other teams surrender to them, thus further enhancing their positions of power. Again, removing vaults would help to simplify these problems and encourage a more fun, competitive war.