Just take the top 16 teams league-wide and quit worrying about conferences anymore. Seed them like a standard tournament - 1 vs. 16, 2 vs. 15, 3 vs. 14, etc. After each round, re-seed them with the highest seeded team drawing the lowest seeded team until you're down to just two teams left. It would make regular season success more important as a few games either way can greatly effect your playoff seeding. If the season ended today, 10 western teams and 6 Easter teams would make the playoffs. Can't say that there aren't a couple of western teams missing the playoffs that are more deserving of making the playoffs than some of the lower seeded Eastern teams.
NBA Playoffs (right now) based on this:
#1 Spurs v. #16 Wizards
#2 Thunder v. #15 Bobcats
#3 Clippers v. #14 Nets
#4 Pacers v. #13 Grizzlies
#5 Heat v. #12 Bulls
#6 Rockets v. #11 Raptors
#7 Blazers v. #10 Suns
#8 Warriors v. #9 Mavs
All above .500. This would have Memphis replacing Atlanta, that's it. Atlanta has a winning % of 45% and Memphis one of 59%. Only non 50%+ team that wouldn't make it is Minny and they are 50% even.