There's alot of threads on this in many forums, so we are not alone (I have the same issue). Let's hope they at least make the windows resizeable so we can get to creating!
HAve you checked the ini file for the editor ?? normally there are config settings for most of the windows in there so you should be able to setup default window sizes in the ini for most of the windows .
For example the Papyrus script window in the SkyrimEditorPRefs.ini
Papyrus Script Pick Window X=668
Papyrus Script Pick Window Y=333
Papyrus Script Pick Window W=490
Papyrus Script Pick Window H=342
SO the window is drawn with a width of 490 pixels x height 342 pixels with the upper left corner of the window placed 668 pixels in and 333 pixels down from the upper left hand corner of my monitor !! Adjusting the position and size is just a matter of entering the correct #s (Note the game updates this position based on the location\size of the window when the CK is shut down)
Pretty much every window is listed in there somewhere so just need to find the one(s) that need adjusting and change them to suit your system !