Institutional repositories are hampered by copyright restrictions laid on them by publishers that are agreed to by the authors. Researchers can, and do change the conditions of their publishing agreements.
Repositories are an important factor for creating 'overlay' journals - where material of sufficient quality is edited and republished, re-creating the editorial function of a traditional journal, but without a lot of the commercial imperatives.
My organisation had issues with iHug customers not being able to use our website - we run a big complex web application. Many many calls to iHug tech support took us nowhere until I dropped an email to their business sales group - something along the lines of, "Shall I tell the 30,000 people in my organisation not to use iHug for the time being?".
It was a complicated problem between d-link, telecom and iHug, but man, it got sorted. In fact, I was so happy with the solution and the communication from iHug I sent the people involved chocolate fish. It shouldn't have only happened after my threats though.