I'd rather see more use of colours than a moving stuff around, the problem for me is not so much with placement, but about clear division and oomph, ie. standing out. Some buttons get alot of use, they get clicked numerous times every time a visitor is on the site, these buttons/links need to stand out above the rest(because a user wants to click them, and often, he/she needs to be able to locate them on the page quickly).
This is something i changed when i wrote my stylish skin, i like frequently used things to stand out, and to see some clear definition between listed items.
Here for ref:
New Design Launched
I really hope my post in the design thread didn't offend, after all i'm not a designer, and i don't know how users view and expect websites to look/behave, but i did hope that in posting the screenshot it might help to illuminate some of the areas that i find make the site harder to use.
I'll be happy to post some more critique if it's invited, but going by the few responses to my post in that thread i'm a little hesitant to, though i still thank those that took the time to provide positive feedback on the post.
And for those of your finding WPSE a little harder to use, in whatever manner, i would advise you to install Stylish and get tweaking, you'll wonder how you ever did without it once you get cracking..
In short, i agree, certain links/buttons do need more prominence/oomph!.. :)