Hey Michael,
I'm not a developer, just a user (and a UI enthusiast). You are correct in that the dialog is too cluttered but you're wrong on some details. Let;s begin with the fact that fill/stroke is not a window, it's a dockable inside a window. This means you can drag the gray bar at the top and move the dockable elsewhere, such as to the main window - or to another window which aleady has a dockable. At that point the window has two dockables and the window title changes to "dock #3" or something similar and no longer reflects the contents of the dockable. So, while ugly, the bar is necessary. If you want to solve this issue you'll need to find a different tack. Sadly GTK seems to not be very flexible so don't expect that to change soon.
Maybe I haven't understood exactly what you have said, but I don't see the issue. At the moment, because there is a normal GTK Window border, it appears to me, or a first time user, that this is a normal window, that the awesome docking functionality that we know exists, does actually exist. (Plus there is duplication which I mentioned on the wiki page).
By removing the top border, you remove the preconceived idea that the user has built up in his/her mind, that all thing with that border are windows, and such are not dockable. This makes them think again when they see it, and hopefully through that they will start dragging and manage to dock it, or use the dock button on the window bar.
I just feel with the GTK Window bar (which can easily be removed), you remove this chance to learn.
Now here's another issue where your design is problematic: You chose to turn the paint / gradient / pattern selector to a drop-down list, while changing the color mode tabs to a button row. Now, a button row takes a single click to change modes, while a drop-down list takes two. So, obviously, we would like to have the buttons for the more commonly used option, and the drop-down for the less used command. I don't know about you, but I use these buttons ALL THE TIME. As for color mode, I rarely change it at all. To me it makes no sense to give it so much space and skimp on the buttons. It would slow my work considerably. If anything, move the color mode to a drop down. The buttons have to stay.
This is something I worried about as well. I feel that without the labels, the icons are not as useful, and it is not that clear that what they do will affect below. Is using a combobox so hard? In fact it is still one click, hold down and release on the item you wish to select.
Of course if I receive the same feedback from others, I can always modify the mockup to have this changed back. I am not saying it is prefect first time :)
Lastly, a general note: you seem to aim for beginner / casual users. I believe in the case of Inkscape this is not the right audience. this is a vector editor, and most casual users aren't really interested in such an application. Inkscape is a professional grade program - at least for certain uses - and your redesing would seriously detract from its usability.
I would disagree with this point. Less clutter and better usability (which I am trying to achieve in this case) benefits all users, whether they are casual or not; and I feel declaring not to include casual users in our thinking is a bad move - we were all casual users at one point were we not?
Thanks for your comments :)