There is some interesting talk about eliminating divisions in the NBA (here and here and here) in part due to the terrible state of the Eastern Conference and in part because of the fact that the three-division system results in playoff match-ups that make no sense. The current system could give the team with sixth-best record the #3 seed in the playoffs.
Of course, if the NBA really wanted to make an improvement in the quality of the game, they would eliminate teams to reverse the effect expansion has had in diluting the talent pool.
A large part of the problem with divisions is the realignment of divisions several years ago, moving from two divisions per conference to three. Having more division championships devalues being a division champion. The realignment has placed an equal number of teams in each division, and moving back to four divisions (two per conference) would make them unequal, but the divisions were unequal before the realignment.
There is merit in eliminating the divisions entirely. Seeding the playoffs based on record alone would make the match-ups much more logical, and there is not very much focus on winning the division anyway. To make divisions really matter, the playoff bracket would need to be completely restructured, and that would create more problems than it solves.
The best solution is to eliminate the division system entirely.