With no .Xresources settings, and all the fonts set only via M-x customize-face, the initial frame gets the settings you tell it, but when you use C-x 5 0 to open a new frame, it does not have the faces you want -- the text is a different one. Attached is an ~/.Xresources that I would like you to distribute with Emacs. Please mention it in debian/NEWS so people find it and can copy it do their home directory and edit it to their own liking.
Perhaps you can install it in /etc/X11/Xresources/Emacs21 ? You might want to edit it some to make it more consistent with the Emacs defaults, at least with regard to the color scheme. As far as the font faces goes, I think that the defaults are horrid and hard to read. These settings are much nicer. It's using the dejavu-dejavu sans mono and it looks GREAT!
There ought to be a configuration option for whether you want a light or a dark screen, perhaps. It can be implemented using CPP macros and #ifdef in the resources file.
I made a few mistakes in the previous. I had neglected the scroll bar colors, and forgot that I had defined 2 background colors, then missed the numeric suffix where it was used. This version should work better.