You said in another thread you were about to give up on Joomla - can I ask why? I have started to use it and as far as I can tell from your list it supports most of the things you wanted above - and anything that isn't there as standard is almost certainly available via an extension.
-Carol Haynes
Hi Carol, thanks for being so patient with me 
In that other thread I listed some of the deal-breakers. The wysiwyg editor is horrid if you ever hope to maintain consistent layout of pages, and when you switch to html mode, it's unusable (try it), so much so the only viable option is cutting and pasting between the browser and a desktop html editor. Strike one.
Then the issue of linking. I didn't realize before it was going to be such a big deal, but use internal linking a lot in whatever I write. having to use links like this http://eee.example.c...;id=26&Itemid=40 is another dealbreaker; even clean URls aren't too good because you still have to look them up every time and they can go stale easily. Strike two.
Strike three is that the sections and categories just seem to be empty vessels. They have no structural meaning and no functionality. And there seems to be no way to predefine page layouts for specific sections and categories. Basically, every time you go to create an article, it's a blank page. I need to be able to associate - automatically or even manually - layouts to sections (or individual articles, at least) to keep the page layout consistent. (It's completely impossible to achieve with a wysiwyg editor).
I haven't given up completely on Joomla, because I've invested much time in it already, and because I really love the templates I mentioned. I can't believe that last third point is a no-go. But the first two definitely are. Installing Joomla is a breeze, configuring it likewise, but adding articles, structuring them, formatting and linking between them is a surprisingly fragile process. Then I saw that all editor add-ons for Joomla are wysiwyg (except one that hasn't been updated for 1.5), and that was where my knees went weak 
-tranglos
I think you are missing some things in Joomla:
1) Install JCE Editor for your editor - it is much better than TinyMCE and you can use HTML (and advanced HTML). You can even embed objects and include PHP etc if you want to. You can download it from the extensions website.
2) Rename htaccess.txt to .htacess and then go to Global Configuration and all the SEO settings to YES and hey presto you get meaningful URLs complete with .html extensions!
3) You don't need to enter any internal links. In JCE Editor select your text and then click the link with the green star - you can then navigate via a section/category tree to the content you want to create the link (which is then automatically updated if you edit pages and change their IDs).
4) There are a number of ways to use Category and Section views on the website - when you create a menu entry choose artcile and experiment with options other than Article Layout.
Re. standard layouts for articles - you can really do what you like - you can even use overlays in JCE to build layers of content, you can insert and style div tags, use tables - you can even import content from Word documents.
Why not just decide on your the layouts you want and then copy the HTML to a text editor and simply paste it in to each new document. To be honest I have looked at a lot of CMS systems and haven't seen any that provide a way of applying standard layouts to each article other than by coding the layout yourself as I have suggested here.
The only thing I would warn about is that if you allow 'front-end' submission and editing of articles Joomla seems to prohibit some HTML and code based content (presumably to avoid potential security issues). This is not the case if you submit new articles and content from the backend.
Also I mentioned Artisteer before to you - it really is a fantastically easy application to generate templates for Joomla/Drupal/Wordpress etc. without having to do anything really by way of design - just choose a few fonts and change a few pictures and dimensions until you like what you see.
If you want a hand just send me a PM and maybe we could arrange to be online at the same time and use a messenger client to chat (I am no expert but I will try) .