1) We're using a discussion board in one of our courses. Now, to be fair, the students and teachers are learning how to use a discussion board correctly. Some students were writing their reflections in Word and uploading an attachment to the Board. That's not good board etiquette and its something that's being discussed. But to make matters worse, Sharepoint's out-of-the-box discussion board hides the attachment from the viewer: you see a small paperclip icon and then have to click twice to get to the Word document. It appeared to the class that their attachments (and therefore, their homework) wasn't there.
2) Working with another group, we were trying to develop a way to manage the Fitness Room. Sharepoint's built-in calendars are excellent and we've used them in some innovative ways. But in order to simplify things and remove options that clutter and confuse, you have to triple-click on a tucked away options page. Yes, that's right; a triple-click. Every environment has its strengths and weaknesses.
Sharepoint is excellent in many respects. Its integration with all of the Microsoft products have really streamlined many of our operations. The combination of OneNote and Sharepoint has been extraordinary! And programming produces some extremely powerful solutions. But it requires considerable background and skill to make things happen. That's not going to easily happen when teachers' expertise doesn't include Microsoft programming.