There is no doubt a Portal brings more value to a business than Intranets of old. No longer a a simple venue for disseminating key corporate news and knowledge in a branded internal website, Portals have become the focal point for many knowledge workers. Key to this success is the orientation devices given to users: Does the User Interface assist users in getting what they need? Does the Information Design make sense to its users? Generally this is called the User Experience. In Portal product implementations, such as SharePoint (but this could apply to any product), one of the key challenges is implementing a great user experience (high usability) and ensuring corporate culture and branding needs are met, while not deviating too far from the base features of the product you're implementing.
Which brings us to our next big SharePoint question:
2) We don't like the out of the box SharePoint interface...can we change it?
The answer is: of course. SharePoint is a web based product and is built upon standards such as cascading style sheets. There are also a core set of templates responsible for driving the majority of the SharePoint User Experience: templates which can be modified to meet any design needs. The REAL question is: how far should you go? You would never think to completely change the user interface of a desktop product such as Word or Excel. Should you really change a Portal product?
As usual, there's no one correct answer. Every company's branding requirements differ. The ability to train employees versus the ability of employees learning things on their own also makes a difference. Deviate too far from the original intent of the product, and you could not only be working against the purpose of the solution, but also undertaking a costly and risky venture.
The key questions to ask are: What are your branding requirements? What is your budget for this type of undertaking? What resources do you have to maintain and enhance the User Experience over time? Do you have the ability to increase training to deal with less than ideal usability issues with the product you're dealing with, or do you have the time it would take to make the product easier to use?
Once you've answered these questions, you're ready to start working. Microsoft has a great white paper on this subject: Branding a SharePoint Portal Site.