I agree pretty much with everything that Urs said in that previous post and find this kind of discussions very useful
There are many good new features in the new theme system http://docs.moodle.org/dev/Theme_changes_in_2.0 and in most cases we do not actually need to /have to do exactly like the guide says. We don't need to use the recommended way to add javascripts to javascript folder, we can for example use layout files like web pages do and add normal script tags there - or add css file tags to layout files - and these files can be even outside moodle itself.
It's good to have consistency to be able to keep main features like headers, main block styles, dialog boxes etc similar looking - like http://tracker.moodle.org/browse/MDL-28198 tries to achieve (in the future when all the yui 2 things are gone...)
What typical cms themes like WP, Joomla or Drupal themes handle better than moodle is still modularity - core moodle is growing all the time like core YUI since people try to build all new features inside the core files while cms systems add optional plugins.
In moodle the capabilities to add/drop/change themes, filters, activities (modules, blocks) and finally in moodle 2 also editors are just great - although partly unfinished.
The main goals for moodle 2 theme changes (set by developers) were:
1) easier theme customisations - both CSS and images
2) simplify core and themes code
3) significant performance improvements
4) solve majority of browser caching problems
5) use YUI CSS foundation
6) allow themes to be stored in separate directory without www access (such as dataroot)
Now when I look back to those goals performance was partly improved by many good changes to caching etc but at the same time YUI css and other YUI stuff spread all over moodle and I actually never wanted to use YUI css in themes and I was wrong in
http://moodle.org/mod/forum/discuss.php?d=131219#p574615
We can select many things in moodle 2 themes but yui javascripts and css are loaded in any case - you can just override the code you don't want to use.
After all there should not be so much difference in designing themes to cms or lms systems. They all have pretty much similar activities (forums, poll/survey blocks/modules, image galleries, repository plugins,...), they all use Wysiwyg editors for editing data and database for saving data. They all are used by different user groups (educational/commercial/...) and they all try to be the best available systems on earth
So you could as well turn that old mantra "Moodle isn't WordPress" to "WordPress isn't Moodle". Moodle has many things that could be improved if things were as freely pluggable as they are in WordPress, Drupal or Joomla. I have used them all
I suppose that our main problem in implementing KISS principle to flexibility of modern web 2 systems (no matter what they are called) was that everything in moodle 1.X was originally so inbuilt that building the new and glorious, fully pluggable Modular Object-Oriented Dynamic Learning Environment took too much developers time with so many old and new features pushing and pulling moodle to different directions... and now we are stuck in situation where developers are tired to even talk about changing some core features to optional features