Mixed divisions could be interesting. Back in the good old days most of the Tourneys I played with Ballistic were mixed, and while it meant novice teams were unlikely to win a division, it gave you a good spread of teams of differing ability to play.
Thinking aloud here, but how about a formula 1 style points system with a handicap element?
Teams get series points from their final positions in the division in that leg, e.g. for positions 1 to 8 they get 10,6,4,3,2,1,0,0 points towards their league total, or maybe 10,8,6,5,4,3,2,1
When you play teams, you score points derived from their league scores, maybe an average of their total score over the series (total points divided by rounds played). So a nov team that beats a successful or pro team in their division get rewarded by big points in the leg, but pro teams the steamroller novice teams don't score big. It would also help compensate if a division ends up loaded with more quality teams. Not sure how points for eliminations would fit in.
I suppose you'd have to throw some figures together and simulate what might happen. The aim would be to keep the league scores close so that pro teams don't run away with the league, and novice teams that play hard don't lag too far behind.
Just a thought.