There is definite "method to the madness" for making UI changes, but afaik there hasn't been a definitive location for outlining the general guidelines on UI changes. Perhaps the best place would be in the Inkscape Developer's Manual, so I've started a section here:

http://wiki.inkscape.org:8080/wiki/index.php/DeveloperManual#Implementing_Us...

Please review and add. I don't think we need exhausting details, just explain what the general motivations/principles are that Inkscape UI developers should strive to follow.

Bryce