The 1990's had teams with large markets stocked with talent at every position. The 49er's, Cowboys, Packers, Broncos, and Steelers loaded up year after year and it seemed like the same 4 teams in each conference were in the mix for the Superbowl.
Then the salary cap and free agency really picked up and the talent pool became more evened up between teams. Combine that with the revenue sharing and smaller market teams could afford higher priced free agents. As a result, more teams became competitive and parity in the NFL began to unfold.
My point is that as long as you secure a spot in the 12 team playoff tournament, you have a shot at making a deep run into the postseason. Teams get hot at the right time and make a run. Look at the examples this decade. The 2000 champion Ravens were a wildcard team that won two road playoff games. The 2007 Giants won every playoff game on the road to advance to the Superbowl. The 2008 Ravens advanced to the conference championship as a #6 seed last season. I'm sure there are quite a few more examples I haven't mentioned.
Homefield advantage is important but look how many #1 or #2 seeds have been toppled this decade. The 2006 #2 seed Ravens lost in their first playoff game at home. The 2009 Chargers lost their first home playoff game. So did the 2005 Colts. Again, there are other examples I have't mentioned.
Playoff positioning is still vital but greater emphasis is placed on what team gets hot at the right time.
#1 seeds that didn't make the big one, during the 2000s (eliminated by):
2000 Titans (Ravens*)
2001 Steelers (Patriots*)
2002 Eagles (Bucs*)
2003 Eagles (Panthers)
2004 Steelers (Patriots*)
2005 Colts (Steelers*)
2006 Chargers (Patriots)
2007 Cowboys (Giants*)
2008 Giants
#2 seeds, eliminated by someone other than a #1 seed:
2000 Raiders (Ravens*)
2001 Bears (Eagles)
2003 Rams (Panthers)
2005 Broncos (Steelers*)
2006 Ravens (Colts*)
2007 Packers (Giants*)
2008 Panthers (Cardinals)
*= Won Super Bowl
You make a great point. The 2000s also saw five franchises reach the Super Bowl for the first time (Ravens, Bucs, Seahawks, Cardinals, Saints). Two have won it all (Ravens, Bucs), so far.
This Super Bowl is the first since '93 where both #1 seeds meet in the big dance. It's strange that, even in the 90s, this only happened twice.