Most organisations rolling out SharePoint want the UI to be branded with their colours and logos. Some take this even further and want the layout of the pages completely redesigned. This is fair enough if we're talking about rolling out SharePoint as a new corporate portal, intranet or an external extranet. In these cases, there may be an important marketing aspect of the rollout justifying lots of UI customisation. However, there are scenarios where customisation might not be worth the effort.
If SharePoint is used as an internal productivity tool only, you should seriously consider to go with the standard look and feel. Just like you do with the other Office applications. You wouldn't even consider skinning Word or Excel to reflect your corporate brand. The focus is entirely on functionality and usability, not aesthetics.
There are some drawbacks of customising the SharePoint UI extensively. You end up with a non-standard implementation that is harder to maintain and support and there are also unknowns about how well a heavily customised implementation will come across to future versions of SharePoint. I'm not saying that branding SharePoint is a bad idea, but you should only engage in considerable customisation of the UI if the branding is really important. It might not always be worth it.
Using SharePoint as a productivity tool in internal teams should be seen as an extension to the other Office applications. It behaves like Office and it looks like Office. Yes, it does look boring if you've spend a lot of time with out-of-the-box SharePoint installations, but so does Word, Excel and the rest of Office. Like with any other deviation away from standard configuration, have a good reason before you do it.