2006 is the only I felt that Smackdown wasn't as good as Raw. Raw that year wasn't all great to me but Smackdown was just a little worse due to Angle leaving and Batista getting injured.
I have a few points to make as to why I feel that Smackdown has been consistently better than Raw but first let me address HHH and Raw at that time.
I know a lot of HHH bashing in the past on these forums is because of what he did from 2003 to 2005. I know Raw sucked during that time and even I have referenced this but I believe HHH is a victim moreso than any of the guys he supposedly "buried". Look back at the Attitude Era for a minute. Who you say were the five central figures of that era? Rock, Austin, HHH, Undertaker, and Foley. Foley is debatable as some people would say Angle. During 2003, Rock left for Hollywood and Austin retired from active wrestling so HHH was the biggest name out there. Undertaker and Angle were never the top guy and you saw on Smackdown, that Angle was injured most of the time. I feel that it was basically HHH and no one else who could carry Raw at the time.
Now, let's get to my points.
1. Teddy Long has been the GM of Smackdown for seven years for the most part. Some say that he is stale and a change is needed but I disagree. Bischoff was a good GM as well as Stephaine McMahon but both seemed like they took a role in their respective brands more than they should have with the latter being more of a culprit. I remember Smackdown in 2003 being more about Stephanie and Vince than anyone else and that simply cannot happen. Teddy Long does what I feel a general manager is supposed to do. Make matches, don't make yourself to be bigger than your wrestlers, and be a peacemaker of sorts when things go awry. Long has done a great job in this role and I believe he will continue to do so.
2. I've never been much entertained through wrestling by talking but more by what you do in the ring even though I know mic skills are an important part as to getting over and being a great wrestler. I've noticed this over the years but more strongly these past couple of weeks. Whether the matches are 20 minutes or 5 minutes, you get your worth and you want to see more especially with shorter matches. I remember watching DiBiase vs. Kidd a few weeks back and saying to myself, "This match was good and I can't wait to see what they do if they give them an extra five minutes." I never get that from watching matches on Raw and that leads me to my third point.
3. If you like wrestlers talking on the mic and advancing storylines through that, then most would lean towards Raw. If you like advancing storylines through matches, than Smackdown would be your cup of tea. Both shows are two hours long and I see a big difference in the last thirty minutes of each show. With Raw, it seems like they are rushing trying to fit everything into the show and it hurts the main event because it will be rushed. You always get fifteen or twenty minutes on Smackdown for a main event and the pace is evened out throughout the show. Raw and Smackdown both have opening segments to start the show where a wrestler gets on the mic and talks about what happened last episode or what's going to happen in the future. Smackdown has that nice mix of wrestling and talking where you don't have a lot of time between matches but everyone gets to say what they need to say.
4. My final point has to do with the midcard on both shows. This is where I will give Raw credit as early on they had Christian, Chris Jericho, Randy Orton, Edge, and Shelton Benjamin having great matches. Then Christian, Edge, and Benjamin got injured and Orton moved up as he won the world title. With Hardy, Carlito, and Morrison, it looked like the IC Title was having a resurgence but then Santino won it. I hated him winning it and it took Mysterio and Jericho on Smackdown to "save" the title so to speak. I never thought much of the U.S. Title and they tried to make it just as important as its counterpart but I believe could never do it. Believe me they tried with best-of-5 or best-of-7 series both involving Booker T but it just couldn't happen although most of the Booker T/Benoit matches were very solid. Ever since then, you just haven't had a great or remotely good storyline for the title. Most of the time it has been defended in multi-man matches (I'm looking at you Kofi) or has rarely been defended at all.
All in all, I have enjoyed Smackdown more than I have enjoyed Raw for those reasons. Raw has had its shocking moments especially this year and Smackdown has trouble reaching that level mainly because the show is taped so people read the spoilers. I just love a good wrestling match that tells a story and Smackdown has always been able to do that for me more consistently than Raw has. To most, Raw is the A-show because it has better ratings and is more entertaining. Smackdown gives me what I look for in every aspect so it is my A-show.