This is probably just a Windows 7 learning curve. I have only been on Windows 7 since March 2012. I felt the same way when I started - sheesh! everything is so weird - why did MS do that?
Anyway, after a month or so, I figured out that Windows 7 wasn't all that bad - I had to adjust (old dog.... new tricks...). I'm fairly comfortable with it now - having spent the time figuring out that the right mouse key does a lot more than it used to, and a few other nuanced changes.
Search Sevenforums tutorial section for an answer - there's lots of good work there. I found this post
that links a few of them. You might be more interested in removing favorites and Libraries than the other so that the explorer tree is top most.
Changing the target in the explorer shortcut can also manipulte the navigation pane.
makes the focus go directly to the explorer tree - it doesn't add or remove any objects - just changes the initial focus.
Edit: huh... took my own advice and found a tut on what I found elsewhre on the web - gee, didn't have to go searching out there after all.
Maybe your needs would be satisfied by putting
%UserProfile%\Downloadsin the explorer shortcut - that puts the initial navigation pane focus on downloads.