Although I could trot out my credentials as someone who has built websites professionally since "cross browser" meant Netscape 1 and Mosiac, I think the really valuable opinions are the web USERS. Yeah, I could dig into their code and design to find some serious flaws, but if the typical web user never notices, then how important is it? For example, I seriously doubt the majority of web users noticed that the drop shadows aren't consistent, and just how many of them even cared?
However, this isn't to excuse the site. It does have it's problems, but clicking around WoW site real quick and saying how great it is* and then digging into a lot of minute problems (and some far from minute ones) isn't very convincing. For one thing, I need to go back and look at each site to see why WoW's side navigation is "a lot of great content" while WotC's is "these weird little text and expanding areas" (or however you criticized it).
The one area I think a lot of people are having in this thread and you mentioned in your video comes down to the fact that the site is designed entirely around current content. The current two Dragon articles, and current two features, etc. are well highlighted and presented (could always use some work, but the site does do a decent job). However, anything past the current two is an after thought. The archive navigation and Dragon/Dungeon indexes are quick and dirty. There are dozens of ways to better present past content (and even some better ways to present current content, for that matter), but this really brings me to my final point.
The site is temporary. Although they did a quick facelift with the 4e announcement, all along they have said that this is temporary (especially the Dragon and Dungeon portions), and that the final site will premiere this spring. In fact, didn't they recently announce it would be the end of this month (or was it next month? Somewhere they gave an actual timeline.) So the current site could be leaps and bounds better, and I'm not holding my breath for the final version to be astounding, but I wouldn't drag them over the coals for a poorly designed site that they intended to throw away less than a year later. Not the best advertisement up to this point, but with limited resources, you can't afford to put too much into a throw away site.
Now, if the final site isn't a dramatic improvement, then go ahead and criticize it. But for now, I can't really bring myself to have much problem with their current one considering it's focus only on current content and the fact that it'll be done within weeks. I just hope they have spent time doing usability tests and such with regular users and not relying on just the web developers designing what they want.
* (Just FYI for future videos, you might want to count how many "greats" you said while looking at the WoW site. I'm not being snarky, just pointing out that with that site being secondary focus, I got the feeling that you didn't have it as written out in your head as you had your wizards.com comments, so you got quite repetitive, just for future notice.
Oh, and the digs at the magazines only being online - even though I agree entirely - didn't seem related to the website critique and just stunk of bias. Makes it easier for people to disregard your valid points when sneak in the invalid ones.)