Umm....sorry, but *why* can't you just theme those areas if that is all you want to do?
I'm really not too sympathetic to theming complaints, seeing as how
I've seen something like 60+ sites launched in the past year with
custom themes -- see
http://www.aeropod.ca/ or
http://www.netsquared.org for two examples off the top of my head.
*Design* is hard. A completely custom look and feel for your website is
hard. Cross browser CSS is hard. Designing individual pages in HTML and
uploading them via FTP is hard. None of these things have anything to
do with Drupal.