The seductive allure of a commercial mega repository is two-fold: (1) everything is conveniently in one place, and (2) a company is taking care of the dreary and expensive business of running it.
Everything seems fine: problem solved! That is until something goes wrong, such as the repository being bought and controlled by a publisher or being threatened by lawsuits by a coterie of publishers.
Then it's important to remember: it's a company, and companies exist to make a profit.
Heh, companies are great. I wouldn't have just had that tasty cup of coffee without them. But, we should be very clear about what motivates companies and controls their behavior. And we shouldn't be shocked if they do things that aren't motivated by lofty goals.
I know: institutional repositories are hard work. The bloom is off the rose. But they exist to serve higher education, not make money, and they part of the academic communities they serve. And they can't be bought. And their universities don't often go out of business. And there are a lot of them. And they are not likely to be attractive targets for lawsuits unless something has gone very, very wrong at the local level.
Copyright is complicated. No one is advocating that we ignore it and just shove e-prints into IR's willy-nilly. Getting faculty to understand the ins and outs of e-print copyright is no picnic, nor is monitoring for compliance. But the battle is easier to fight at the local level where one-on-one faculty to librarian communication is possible.
For self-archiving to flourish in the long run, institutional repositories must flourish. By and large, librarians establish, run, and support them, and they are the quiet heroes of green open access who will continue to provide a sustainable and reliable infrastructure for self-archiving.