As a general commentary, when you talk about a GUI you are actually talking about 6 billion opinions. This is comparing your driving skills to everyone else's, your driving skills are great, but their skills suck. I have to agree that the average Moodle interface is not that good, but I suggest that is a result of the structure imposed by blocks and modules. I suspect, although I cannot confirm this, it is actually based on the older PHPNuke or Post-Nuke interface or something similar. These were, AFAIK the first of the "modern" (about 1997-8) truly OOP PHP based CMS' and influenced just about everyone in the time period that Martin was first designing Moodle. Having said that, this in no way implies anyone copied anything, just all our design structures are influenced by something, usually quite a lot, and we do not even realise it. This is also called social inertia, for truly radical designs are few and far between and are usually derided, sometimes for decades, before they are seen for what they are and their impact is properly assessed.
Moodle sites tend to be staid, secure, and non-controversial. Considering their essential product, is it any wonder. Being an older male, for me the three sites you put up are incredibly busy and quite tacky. A good design for me is clean, clear of clutter, easy to view and easily intuitive. For me, the original idea of Administrative matters on the left, site matters on the right and core materials in the middle is OK, but inflexible. Some of the Moodle 2.0 themes move away from this and allow a number of alternatives. This is a step in the right direction, but we must always consider the dangers inherent in taking too many risks. You may want to look at this site, Vincent Flanders is an incredible observer of human perceptions and taste. Always an entertaining read, he really makes us consider what we think is good design, if we look, that is.