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What skill are we talking about? The skill of mages fighting mages, and warriors fighting warriors? It would make more sense to have all mages fight all other "power" units to determine the best based on skill.
So, by "skill," you mean ranking participants based on the results of games within a group of factions.
Added 3 minutes later
There's another interesting option: you could divide them into two groups without any preliminary ranking based on rating, etc., and in each round, players from different groups would face each other, i.e., strength against magic.
The first round would be a random draw. Based on the results of the round, participants would be distributed within each group based on the points they earned. Then, a standard Swiss system would be used, meaning players with the same number of points would face each other, but two players wouldn't be allowed to meet again.
After 3-4 rounds, the strongest players in each group would be identified, and a playoff would be held between them.
P.S. Although, I think that playing strength against strength, as well as magic against magic, is also interesting in the first stage.