You're right, the whole system does need to be overhauled. It's not just inconsistency that's a problem, though. It's the blatant favoritism that really upsets me.
When Jordan shoots a fadeaway, gets brushed on the arm after the release, and goes to the line for his bonus.
When Kobe gallops into a jump stop, takes another step, and dunks.
When Shaq throws his elbow into his defender's face, shuffles his feet, and dunks.
These are all plays that any other player would get called (or not called) for. In the NBA, the superstars are above the law, most likely because the players and the league can see a tangible benefit in letting them score a ton of points.
I don't think there's a league-wide conspiracy or anything, but I do think the refs in the NBA suck horribly when compared to their counterparts in the NFL, NHL, and MLB.