SharePoint offers a lot in the way of content management and building communication between colleagues. It does both of those well, but the main problem with SharePoint is visual design and usability.
No tool is perfect, but SharePoint has some underlying problems with the way that it was developed, and these choices make visual changes awkward. In short, the product looks as if it was designed and built by programmers without consultation of a visual designer; this assumption may not be true. It could be that limited resources were put into the application in the early stages, but the demand and popularity of the tool has resulted in the software growing quite quickly. That said, the new version of SharePoint is much easier to change than its predecessor.
SharePoint is built using tables; CSS is used, but it is limited. Due to this, it takes considerable effort to make visual design changes. The difficulty is magnified when faced with attempting to use the same design in the Administrator-level pages, which have a separate visual design and set of pages. I am hoping that the next version of SharePoint is table-free and promotes easier visual design changes.