I now have to scroll down one whole page in order to open the tag-specific pages. I find this disturbing.
This is how it was and should be.
After discussing this a bit internally we've reverted this change for now and done a build to push. The change isn't just moving these things, there's another component to it you'll see soon, hopefully next week.
There may yet be a shuffle of the sidebar associated with that, we'll see when that comes...but we will keep the favorite tags as nav use case in mind (I often use them this was as well) when deciding what to do. Not tagging this status-completed because I can't promise it'll be a permenant change.
Here's a bookmarklet for you that makes them come to the top and try to catch your eye:
I'm no fan of favorite tags myself, but I feel that the tags should be back where they were. SO's ads are only effective since we add good content. We don't really need to be shown the ads--we've seen them millions of times. I know that's not going to happen, but hampering our productivity(hiding the favtags) with an ad--one that's pointless to show us-- seems nonsensical.
Update: If you like this so much that you want it done to ALL tags,
Option 1: Move the tag container to the top
How to use: Drag this userscript to Chrome, Firefox (possibly Opera and IE). Chrome will automatically convert it to a Content Script.
Currently, only http://stackoverflow.com/ is added.
Not Enough jQuery
The previous code was written in pure DOM, because that's the most straightforward way in a Chrome extension. For GreaseMonkey scripts, jQuery can also be used:
Option 2: Hide the ads
In Firefox, I'm using the following UserStyle (Stylish (also available in Chrome, btw)):