OK so lets say that we start the first season with 4 teams from each Pro league, filling the extra holes in the pro leagues with extra promotions, etc. down the chain.... then after the season, keep all playoff teams in the WPL and relegate everyone else. This results in, say, the following distribution of teams (non-playoff WPL teams) being relegated:
2 APL
3 EEPL
3 WEPL
0 USAPL
2 CPL
0 SAPL
3 OPL
3 SEAPL
APL and CPL are simple, you relegate the two teams that came from there back there and take the champions.
USAPL and SAPL , you take the top two teams and promote them. The extra promotion continues down through the tree, leaving a gap of two empty slots at the AA level which are filled from the minors just like they were CPU spots.
EEPL, WEPL, OPL, SEAPL: promote the top two teams from each of these regions, just like from the other leagues. But stick the extra teams from the WPL back where they came from, and as a result RELEGATION FROM these pro leagues is increased appropriately. Instead of sending down 4 teams they'd send down 5. The excess relegation would have to continue on a path down through the AA level, where one extra team would be sent into the minors system without a replacement coming up. At that point (if not at every level) we're not talking about demoting an extra human team, there's already CPU teams disappearing so it's just a matter of promoting one fewer team from the minors.
This is the only way I see it working and not pissing everyone off.
The only potential downside is that it might not always be truly the 'best 32 teams', as the promoted teams from weaker leagues might kinda suck compared to the 3rd-4th best teams in USAPL and SLAP who don't get into the WPL. But you can argue that's good for the game too -- the top teams need a few easier games as breaks in gameplanning so that they can play in a tournament or two without completely burning out. I'm not convinced that having the true 32 best teams in a league is the best thing for the game, as those teams might reduce their tournament participation and/or burn out / gut more frequently.