It seems like things in wrestling often end up looking better in retrospect than they did when they were current, 5-10 years from now people are probably gonna be saying "remember the PG Era when D.Bryan and Punk was running shyt on Raw and putting on classics every week

"
But with that said, Smackdown during 2002-2003 was G.O.A.T. Raw wasn't even close. Those Angle/Benoit, Eddie/Chavo, Edge/Rey combinations EVERY SINGLE WEEK was something to behold. Also, the rise of Brock Lesnar was fun to watch.. just overall, great, great stuff. The best thing over on Raw was a PRIME Trish Stratus

starting in 02' when she would wrestle every week in those tight ass pants and low cut tops, she was on another level.
The Ruthless Agression Era is looked down upon because it was a transitional period for WWE at the time coming off the Attitude Era which was other wordly, and Rock and Austin weren't around EVERY WEEK as the superstars of the company, and they were searching for the next guy to carry the ball.
Remember when it seemed like they were having this match every week after the initial WWF draft
I would say Smackdown started to fall off around 2004 when they started to debut the worthless big guys like Matt Morgan, Nathan Jones, Luther Reigns, Mordecai, Mark Jindrak, and A-train.
EDIT: Remember when they botched and made the announcement of Undertaker vs. Triple H at Backlash for the Undisputed title

had them nikkas face off in the ring and everything, then they changed it to Triple H/Hogan

[ame="http://www.dailymotion.com/video/xjzy1s_triple-h-attacks-the-undertaker-22-4-02_sport"]Triple H attacks The Undertaker (22/4/02) - Video Dailymotion[/ame]