Given the turmoil of conference expansion, it's no surprise that the NCAA has made changes to the way that the tournament is seeded. So one big and probably smart change is allowing conference teams which only met once during the season meet in the tournament earlier than before, as early as the third round.
Presumably, the NCAA is still counting the play-in games as the first round, which would mean, for instance, that Duke could play State in Greensboro in the round of 32 (assuming that the teams had only played once during the regular season of course). Top-rated teams from the same conference could meet earlier, and in the same regional, too. But if the teams have played three times, then they can't meet until the regional championship.
It's not just the power conferences (Big 12 excluded) which have expanded to the point where a round-robin schedule is no longer possible. The C-USA is up to 16 and the A-10 is now at 13.
Of course, a lot of the old C-USA has moved up, with some now in the American, so the old C-USA it ain't what it used to be. But at least six conferences are in the same boat. Making adjustments is smart and necessary.