I think the strongest argument for preserving the conference alignments is that it builds rivalries.
You can see the easy counter-argument to this though, right?
I can argue easily that it prevents rivalries.
The East / West split prevents us from getting to see LeBron vs any number of West stars -- Harden, Durant, Chris Paul, Griffin, etc. It prevented us from seeing LeBron vs Kobe. In any given year, we can only hope for one of those matchups.
I think there's a strong case to be made that if you get rid of conferences, we'll be more likely to eventually see a more interesting variety of matchups between the various stars of the game, instead of watching LeBron spend 3 straight rounds facing tomato cans, not to mention settling for Paul Pierce trolling on the Raptors as the highlight of the Eastern Playoffs (much love to Pierce).