Hate to admit it but I agree with thecoffeecake on this one. I didn't like it at first but you need to think of it with the division in mind. It just so happens that the two best point totals came out of the same division and that itself puts a lot more weight in winning your division during the regular season. Once you take care of the best teams in your division, you need to face the winner of the other to have a shot at the league championship and I don't see anything wrong with that.
The one thing that I could see making this system a little more refined would be more games against your division teams, but the whole home/away scheme with the other conference kind of hinders that.