I'm not sure thats true. How many years have the Pats, Colts, Eagles, Steelers, etc, been sitting at or near the top of the league?
The Eagles had a 5 year run (2000-2004) that just happened to coincide with a severe downturn in the NFC East. They were very good but never quite complete enough to win a championship. They have been fairly ordinary since their Super Bowl run.
The Steelers are a roller coaster. Two years up, one year back. Hardly "at the top of the league", even during their Super Bowl run. Outside of 2001 and 2004 (jury still out on 2008), who considered the Steelers a powerhouse? Their system is good enough to stay competitive long-term, but not at an elite level.
The Colts are interesting in that their run got going when they joined the AFC South. Particularly on offense, they have owned the division which generally gives them lots of room for error. While the Colts obviously have been an elite team, they were fortunate to be in the perfect division for them...low scoring and weather neutral. They are only 7-6 in the playoffs during this time and are a 2nd half miracle from being 5-7 with the "Goober is the best QB never to reach the Super Bowl" conversation ongoing.
As for 2008, I don't think people realize how close the Colts were to being out of it. Their margins in their first 8 wins were 3, 4, 28 (Ravens just didn't show up), 3, 4, 6, 3 and 4. Give them credit for pulling out wins, but I don't think Dungy has left the cupboard quite as full as he thinks.
The system is supposed to push teams back towards the middle, but I'm not sure it actually does that.
You are correct that a few teams seem to be able to keep their heads above water (.500 record) and a few teams can't get out of their own way. That doesn't mean the system isn't pulling them back to the middle. Worst to first is pretty common and even the Colts (outside of fortune smiling on them in the 2006 playoffs) are regressing to the mean.
Even the Pats feel this pull but Belichick seems to be able to resist it. Is there any reason to believe that the Pats won't be prohibitive favorites to win it all in 2009? Just like 2004, 2005, 2007 and 2008. That is a 5 year run on the heels of winning 2 Super Bowls. The next real test for the system will be when Brady and/or Belichick move on.