Divisions and rivalries have been apart of the NFL forever it's going to be hard for the league to break away from what has been such a tradition over the years. The current system certainly has flaws when you can have a 7-9 team make the playoffs like Seattle did a few years ago and have teams like NE in 08 and Denver in 85 miss the playoffs with 11-5 records.
Your fate is basically determined by the strength of your division. The Cowboys have had opportunities to make the playoffs the past 3 seasons entering the final week with only 8 wins due to playing in a weak division. We saw a 10 win Cardinals team miss the playoff last year due to playing in a strong division.
It will be interesting to see in the coming years what changes the NFL makes to the playoff system but adding 2 more teams to the current system is going water down the playoffs with at least one losing team having an opportunity every year to make the playoffs.