Read with interest George Siemens post on creating simple information sharing environments http://www.elearnspace.org/blog/2009/12/12/using-technology-to-improve-collaboration/. I just designed a course for St Thomas University using open source tools like yourself for CCK08 and 09.
I am using Google to make most of the functionality work ie Alerts, a Forum, and WordPress for blogging, posting papers. I went open because STU uses WebCT and is switching over to Moodle and I still have not been officially hired yet so I have little time to learn a new LMS.
This brings me to my second point of your point of simplicity over complexity. You note SharePoint problems. Yes it is complex. But it is a useful toolset when trying to organize complex business and making information findable. The portal aspect of SharePoint may be its greatest strength because it does not require much skill to learn to add sites, lists and libraries with standard navigation elements, thus making it easier to find things. I have found after assisting several organizations cleaning up their SharePoint implementation was that they continue to folder their records, treat SharePoint as a fileserver instead of a portal/intranet, and fail to apply metadata to make documents findable, sortable and viewable (ie usability and findability).
You note that I favour SharePoint for the business, but that is because I have seen the power of integrating Project Management, records management, document workflow and publishing, status reporting, and communications (SharePoint can even issue SMS messages!). At the same time, I can also go open source.
One aspect of my STU solution is no grade book. This is a weakness. Wouldn’t a student love to see a grade at the end of my commentary about their paper, rather than have to go to another system to see this confidential info. I have criticized Desire2Learns LMS because of the difficulty of assigning “grades” to discussion posts (RMC does a combined quality and quality metric for discussion forums).
Ultimatley, you have to decide what the information management problem is, what you want to get out of the solution, and what you can afford. Some days it may be SharePoiunt, other days it may by a Google solution.