The centipede was happy, quite,
Until the toad for fun
Said, 'Pray which leg comes after which?'
This worked her mind to such a pitch
She lay distracted in a ditch,
Considering how to run.
-George Herbert Palmer
It's entirely possible SharePoint offers the best out-of-the-box experience of any product Microsoft has ever released. It's just Next-Next-Next-Next-Finish and you have a Portal to turn your webmasters loose on.
SharePoint offers a lot of power. So much power that it can often be in danger of not getting used at all. There's a hierarchy to SPS Portals, Sites, Pages, etc. There are area pages to aggregate information, groups, audiences, topics, “Best Bets,” and so on. There is so much to do, that an organization can spend all its time “planning” how to deploy a portal and never get around to actually doing it.
There is a story about a college, perhaps apocryphal (Larry Wall seems to think it's UC Irvine)
The college was building a large addition consisting of several buildings and a large quad area. After the buildings were completed, one of the Regents visited. He asked why there were no sidewalks between the buildings?
The college president replied that the architect had a good plan - open the buildings without sidewalks, let the students walk over the grass. Over time, trails will develop along the most common paths.
Then come back in a year and pave the trails.
Treat SharePoint the same way - lay out a basic hierarchy, some basic structure and templates, then simply let people start using it. Let them add sites, pages, content, lists, and so on. Let it build, let it grow. After a period of time, start reviewing the SharePoint reports and logs - then the areas, groups, and other aggregations you need should be apparent. If you need additional structure in the Portal, you can add it. Train the topic assistant and see what it turns up. Review help desk pain points and address those in the portal structure.
But all this time your users have been doing what SharePoint was designed to do - collaborate.
SharePoint Accelerator for Intranets (good background info on SPS)