I've been looking at all the ways that you can actually create new functionality over than the base functionality of Sharepoint. Most of this is around actually displaying the content in a portal environment on a public facing web site in a way that external users are used to.
Internal users of the portal will be comfortable with the Sharepoint look and feel and branding is not at the top of the priority list on portals. Public presence is all about branding and content and rendering sharepoint pages takes away from the branding of the site. There are plenty of ways to completely control the rendering of the site and Chris Johnson's post does a great job of explaining the pros and cons of both.
This issue actually came up at the Perth Sharepoint User Group on Tuesday and pretty much every there agreed that the best way to do this was to write custom web parts and take full control. Sezai from Vivid Group will be presenting at next months meeting and will focus on some of these issues so I'm looking forward to his approach to this.