I’d like to see a ranking/matching system like in LoL or Starcraft, where each alliance is placed in a tier from Bronze 5 to Diamond 1 (Major tiers being Bronze, Silver, Gold, Platinum, Diamond and sub-tiers 1-5 within each major tier) plus a separate Master tier for the top 50 or so. Every 3 wars, divide all the alliance into groups of 4 from the same tier and have them play a round robin among themselves. At the end of those 3 wars, the team with the best record is promoted to the next tier up and the team with the worst record is relegated to the next tier down (If 2 alliances have the same record, the result of their war determines placement. If 3 or teams have the same record, total points won determines placement). Loot would increase with tier just like in raids.
I believe this would make wars feel more dynamic and important, while simultaneously helping with matchmaking in the long run. Currently each war is an isolated event which yields mediocre loot, and therefore doesn’t feel impact on the game overall. Admittedly, transitioning to this system could make proper matchmaking harder initially, but would improve matchmaking once alliances got settled into appropriate tiers. This would add mid-long term goals for alliances, and create a feeling of story and progress.