I think there's lots of things you could do regarding that. Maybe add a decent chunk of regular season TV revenue to the postseason pot for rounds beyond the first or something. I don't think it would incentivize mediocrity, at least for teams who aren't the Marlins.
I still believe the best solution is 32 teams, half the teams get in, the regular season is cut back to 150 games with fewer offdays and a balanced schedule, and all playoff series are best of 7. Playoff pool money only extends to teams who make it out of the first round. I like the top seeds picking their opponent idea, so maybe add that in too. You could let selections be from either league if you want to spice it up even further.