So what is your solution? Pointing out the obvious effect of an uneven draw isn't exactly splitting the atom.
1. I already mentioned one solution - don't have percentage as the first time breaker for ladder position. Should be head to head records.
2. If you played the previous years wooden spoon team as a double up, then the next year you only play current years wooden spoon team once the following season.
3. Over a 3 year time frame teams play each other and equal number of time (or at least close to).
4. And every team plays each other once prior to double up games.