You’re going to have to go with some plugins.
The WordPress page editor is dog slow.
Throw more resources at it and/or disable some functions from showing under the “Screen Options” tab. It should not really be slow unless your have a ton of people working on a ton of pages at same time, if you can clarify what/why it is slow.
You can’t drag and drop pages around to change the hierarchy
You will need a plugin for this , like http://wordpress.org/extend/plugins/simple-page-ordering/
Nothing maintains section numbering, like section 1.1, 1.2, 1.2.3.
You have two options here, create a custom field meta box called ” Sections” and enter a number for the value on each page, this is simple to query and display, but does not have any built in hierarchy. Option 2 would be to use categories ( or a custom taxonomy) for pages, and have them as a hierarchy ( this also allows for easier slugs), or just use a CPT.
I haven’t found a way to build an automatically-created table of contents on the right hand side.
There are various plugins for this, search wordpress.org for “TOC”. Or if you use the methods mentioned above you can use some built in WordPress functions ( esp if you create a section taxonomy).
I’d like to have a tag to highlight and indent code.
I like this one, http://wordpress.org/extend/plugins/syntaxhighlighter/, but there are others that are good on .org.