OK, First thing... The way IE handles memory allocation to tabs means that there is a serious hit to resources each time a new tab is opened (I've encountered anywhere up to 5 second waits even with add-on's disabled). The issue first occurred in IE8 which Microsoft themselves acknowledged that the performance hit was the result of how they implemented the mechanism. As such, the issue still remains in IE9 and unfortunately this really undermines some of the speed of the browser. In addition, after running some benchmarks loading the same pages and doing downloads between the browsers... IE still requires more resources and memory than Chrome and Opera - again with add-on's disabled. The browser's GUI has destroyed any comprehension of me considering it (the heavy clunky thing it is).
As for the user-interface itself, the serious usability problems (as I see them) come in many forms:
1) They have stripped the ability to be notified about RSS and Atom feeds directly on-page from within the address bar, this means you manually have to FIND the URL and enter it into the address bar (or browse to it) to subscribe - this also means that unless you seek out the syndication feed, there's no indication it exists.
2) IE's decision STILL to use Refresh and Stop as separate buttons just increases the amount of on-screen bloat, granted it's a small thing but other (better developed) browsers combined them as they both operate as separate states and don't need to be separate in the UI.
3) The mechanism for opening tabs and the position in the address bar is hideous, you have to physically drag and expand the available space for tabs in order to assign it the space required to perform. You shouldn't have to fiddle with the UI every time you want to either assign or reduce the whitespace usage.
4) The navigation icons are a clear example and case of mystery meat navigation, you have to physically click each icon to discover that one navigates to a page, one opens a popup and the other opens a menu - whatever happened to consistency and not surprising the user with inconsistent events.
5) The bookmark / history bar hovers over on the right hand side, but when you pin it to the window it suddenly jumps to the left (rather than the right where it started), this is inconsistent with how the UI has been developed (toward a right hand side management style).
6) The layout of the menu system is nothing short of hideous. Functions that were previously in menus like Edit suddenly find themselves in a now random "file" menu which absolutely doesn't match convention within software GUI design standards - it's like they decided to go against years of common practices.
7) The downloads dialog is inconsistent with browser conventions - where downloads should be tabbed in the same dialog as history / bookmarks / etc. Every other browser does this... IE9 produces a poor and unnecessary modular window for it - it's just a senseless and thoughtless implementation.
8) As for the label "F12 developer tools" (which will make absolutely no sense to the average browser user) - why they didn't follow a consistent convention and just label it "Developer tools" and have the F12 as a keyboard shortcut (visually) like with every other icon, I'll never understand.
I could keep going on about it, or list all the other complaints I've seen and had by other people who've used the software (who I talk too). The rendering engine is much improved, the GUI is a clunky poor imitation of better browsers. If they took UX seriously (for example) they would have at least put the address bar below the tabs to ensure the convention of the address bar being relative to the tab being used (rather than just having it dynamically change onclick).