2 things that came to my mind:
Although the tournament is mainly about the ability to limp into the next stage, it could be nice if a soloing player could choose the next variant. It would provide some incentive to risk more. Of course the winner would be bound by the number of advancing players. If the game ended in a draw, a default variant would be used. So if there was a 3 player variant after solo in classic, the winner could choose from Hundred, 1066... and if there was a draw, Hundred would be played.
Double elimination. If there were many intermediate steps (say 7-5-3 player variants), many people would advance to the next stage. Therefore, one big unbeatable alliance could be formed at the start of each game that would steamroll the remaining minority, thus sucking out all the fun. One way to solve this would be to have less steps. The other one is double elimination.
Say we start with WWIV, 35 players. 19 players advance to Haven, 16 players fall to 2 Migraines.
From Haven, 9 players advance to Known World 901 and are accompanied by top 3 from each of Migraines. Losers from Migraines end, 10 losers from Haven play Modern II.
Top 7 of Known World and top 4 from Modern II play Crowded. Losers from Modern end, 8 losers from Known World play Karibik.
Top 5 from Crowded and top 2 from Karibik play Classic. Losers from Karibik end, 6 losers from Fall play Imperium.
Top 3 of Classic and top 2 of Imperium play Ancient Med, losers from Classic Rat wars.
Top 2 of AncMed gets to play Hundred, while the winner of Rat Wars (rats fight till the end!) play loser from AncMed in yet another Rat Wars, whose winner gets to Hundred.
Winner of Hundred is winner since we don't want to play 2 player maps and so the double elimination is eliminated from the final step ;)
That was just my rough idea, the parameters are debatable, as well as the moment when to eliminate the elimination (can't get enough of it :)