The changes aren't too bad - I've seen worse.
All I'll say:
1) Far too much white - hurts my eyes when viewing for long periods
2) Bars of solid white down the side also too big - I assume they are going to be filled with full height, multi-colour flash advertising in due course though (please don't)
3) Picture at the top of the article is too big - the one in the "UK flights CRIPPLED" article is 429px high and I can only see 2 lines of the actual article (3 once notice about cookies is closed)
4) Why is the section the article is in shown in big letters on the top of the right hand bar. Couldn't you make the image smaller and put it there instead. The section isn't needed as it's highlighted on top bar instead
5) Related topics should be at bottom of article really as you'll be looking for related topics AFTER you've finished reading the article
6) The search box isn't very big, you could swap entire nav bar for search bar and include other options for searching too
7) The images in the nav bar hover are too big too - couldn't you put the text alongside smaller version of each image? I know you could probably only fit 3 articles in but you could have 2 rows and fit 6 articles in the same space!
8) I know The Reg gets money from advertising but the advert at the top of each page is taller than the red header bar on each page. Surely it should be the other way around?
I'm sure I'll spot other stuff and post about that when I can