The learning curve is steeper but the flexibility is high.
Bonus for being able to render mathematics in your docs.
Edit -- Also, I agree with you about the learning curve. Although it's very easy to get good-looking docs if you use one of the canned documentclasses and built-in commands, once you start to stray from those you're in deep water very quickly.
How long are we really talking about?
So, we're talking about a doc that's getting a little too cramped being just a plain text file, and which might grow longer as time goes by.
Thanks for the heads-up.
The POD docs I see as html are just single long html pages. I realize this is just an implementation issue though.
http://www.literatureandlatte.com/scrivener.html is a combination outliner/editor for OSX. Most of its features are focused on allowing you to manage a lot of different bits of a larger document. There's a full XSLT generation engine inside it so you can get it to generate just about anything you want if you're willing to roll up your sleeves a bit.
http://fletcherpenney.net/MultiMarkdown is a simple markup syntax (derived from Markdown) which Scrivener supports.
Scrivener and MultiMarkdown together generate HTML or LaTeX from the base document, so you need to use something like http://www.uoregon.edu/~koch/texshop and http://www.tug.org/mactex to get something worth printing.
DITA is an emerging documentation standard. It uses XML to describe the content and structure of a document. If you write your documentation in DITA XML, you can render it to PDF or online help easily. Yes, DITA is a little verbose.
