I think it would be much better to use xtemplate for the template system
I have seen this in LDU ( www.neocrome.net ) , and it's really simple when you want to edit template.
Each section has its own template file and you ay simply edit the temp file to edit the whole site.
There's no need to meddle with PHP codes, as they're all handled by xtemplate and you only design !
Please take a look and see if it's better to implement that into the new versions of Moodle or not !