It would have to be balanced.
We could say.
1st, 3rd, 5th, 7th, 9th, 11th, 13th and 15th from the current game in one league. (8 Players) + 1 from the waiting list = 9
2nd, 4th, 6th, 8th, 10th, 12th and 14th from the current game in the other. (7 Players) + 2 from the waiting list = 9
The main issue you could get is a "Well he only won because I was in the other league and his opponents weren't as good" etc.
But I do like the idea in principle.
You could argue its the luck of who you end up with, I mean we already play the "luck of the draw" card in the respect of the draft order.