It's been that way for a few years in the Big East, and I actually like the way the Big East tournament is set up. It uses a shocking concept - actually giving a real weight to the regular season.
They didn't want to wear out their best teams (and hurt those teams' NCAA chances) by making them have to play 4 games to win the conference tournament. It's not fair to the really good teams to have to play more games than similar teams from other conferences just so that a couple of really crappy teams can get a bailout chance at a title.
It also reduces the chances that a really crappy team (like DePaul, Rutgers, etc) sneaks in a gets a bid and potentially takes a bid away from a stronger bubble team from the conference. Though that's not really part of the reasoning.
So, they came up with a system that allowed their top 4 teams to only have to play 3 games to win it, but also still allowed the entire conference a chance to win. Sure, it's not equally "fair" to all the teams. But basically, I don't see a need for more "fairness." That was the point of playing the regular season. Is it fair to the teams that played the best all season to have the slate almost completely wiped clean and have to play a single-elimination conference tournament? No. The worst teams had their chance to make their tourney lives easier by winning more regular season games. They failed to do so. They don't deserve a nearly-complete "do-over" in the conference tournament.
Granted, I'm also someone who thinks there are too many teams in the tournament already. Really - teams who go .500 in conference don't deserve a chance to be the conference (or national) champion in my opinion.