The transparent menu doesn't bother me. I think it looks kind of nice, actually, as do the new menus with the blur effect.
The transparent menu as you see it now is a massive improvement over the one in earlier developer seeds. A lot of developers bemoaned it, although I quite liked it. They did have a point that it was quite difficult to see the text on it when you used certain desktop images, though. So Apple upped the opacity a little and now it is perfect, I think. I much prefer it, in fact...
I thought exactly the same about the blue dots, but I got used to them after a while. And I quite like the new dock over all.