If the clubs can't afford to pay more imo they should have less affiliates.
90% of the minor leaguers are "fillers" anyway and while sometimes a late round draft becomes somebody most don't.
If pro ball says it can't afford to pay restrict the draft to 20 rounds, limit the number of affilates to 5 and then pay the remaining guys better.
I think teams could cut their number of minor league guys by 30% without missing much.