One of the biggest changes I've noticed thus far is the annoying location bar. I say annoying, since it's just way too busy for me, especially as it does the highlighting of text as you type. It's a completely different paradigm than how I've become accustomed to using my location bar - I tend to hit ctrl-l, type a few letters of the url, and then use my arrow keys to select the appropriate one. The new location bar seems to be designed around users using the location bar as a search field. To address the business, I'm using the oldbar extension, that goes back to a single line display, that doesn't highlight as I type. I've also set the option in about:config so it doesn't search my history or bookmarks.
The lack of highlighting of secure websites is an interesting decision. Firefox 2 used to display a yellow location bar, as well as little lock when you accessed secure pages. From what I've skimmed, this appears to be due to inconsistency among various platforms. Secure sites now have a blue background behind the favicon (which is now a button that displays more information about the site when clicked), as well as the lock icon in the lower right hand corner. Not a huge fan of this, since the blue highlighting of the favicon is much more subtle than the yellow highlighting of the location bar.
Password management has also changed. The linked blog post discusses how the modal dialog asking to save a password was bad, but the one area where the modal dialog excelled was that I could easily navigate it from the keyboard. The feature is nice in that you don't accidentally save wrong passwords now (as in you don't have to make the decision to save before you've seen if you typed your password correctly). They did have the foresight to provide keyboard shortcuts though, so it's more just a matter of my having to learn some new behavior . . .
Other than that, I haven't noticed any other changes that irk me . . .