You're talking about the site from a design perspective. We are talking about it from a user interface and usability perspective.
YouTube is way more usable now. The side menu is gross, but do you remember how playlist controls used to work? That fucking bar at the bottom of the screen with tiny ass buttons? Holy shit, what a horrid UI.
Old-style channels AKA MySpace 2.0? The new One Channel design is FAR more usable.
http://i.imgur.com/1Se60Th.jpg
http://i.imgur.com/9j4plmk.jpg
Kill me now if you think the top one is better and more usable.
I can agree YouTube stutters now more than it used to, but it also has more users and HD content than it used to. I've seen what it takes to deal with bandwidth and I don't envy YouTube's backend/CDN engineers at all, they have a far harder job of it than almost anyone. The fact that it's even online without constant Fail Wail pages is a marvel of internet engineering.
Where's the gun to kill you with, Andy? Because for me, personally, I prefer the top. It may not be "Web 2.0"/hot for you, but I am a man of 90's web design. So long as it loads fast, doesn't have me side-scroll and doesn't look "busy" I'm fine with minimal "my first webpage/Myspace page" design. Drop the left panel/"popular on YouTube," drop the right "channels" panel, drop the top bar. Leave the videos, leave the related. Link the profile of the author/uploader under it so I can click that to see more of their videos. Final usability destination.
'08 design

X-men

Adblock and Youtube Centre? I'm sure your Google Gods love you.
Bottom looks clean there, but that's because Andy is using extensions to remove some of the bullshit Youtube has, so he's cheating there.
The top looks bad, yes. It's using a flash player, which the one good thing Google brought to Youtube was the mandate of future webstandards.
Drop the "login and rate" box. Drop the comments. Drop the director videos bar. Move the "From:" info box to where the "login and rate" box was. Youtube would've been fine there. Granted, it'd need a UI and standards overhaul but at least it wouldn't look bloated and full of shit that no one cares about.