What is wrong with the cups system used for raiding? Can’t this be used for alliance wars as well? Let’s have a rating count for alliances that is not tied to titans or trophies. Have this as a third rating system for the leaderboards.
Give everyone some score today (maybe start with the titan kill score). Then, adjust the score based on each war win/loss. If you win, you gain score, if you lose, you lose score. If you beat someone with a much higher score, then their adjustment is bigger (like with trophies). That way, people who keep winning will ultimately be matched against someone who is their level. People who keep losing will be matched down with a better matchup.
There are many factors that affect an alliance’s performance in wars- roster depth, player participation, team coordination…let the people who try hard fight other people who try hard. And let the casual people fight wars against other players who are not hardcore.