PubMed & PubMed Central are wonderful resources, but not nearly as resourceful or wonderful as they easily could be.
(1) PMC & UKPMC should of course be harvesting or linking institutional repository (IR) versions of papers, not just PMC/UKPMC-deposited and publisher-hosted papers.
(2) Funders should be mandating IR deposit and PMC harvesting rather than direct PMC/UKPMC deposit. By thus making funder mandates and institutional mandates convergent and collaborative instead of divergent and competitive, this will motivate and facilitate adoption and compliance with institutional mandates: institutions are the universal providers of all research output, funded and unfunded.
(3) IRs should mandate immediate deposit irrespective of publisher OA policy: If authors wish to honor publisher OA embargoes, they can set access to the deposit as Closed Access during the embargo and rely on providing almost-OA via the IR’s email eprint request button
(4) Funder mandates should require deposit by the fundee — the one bound by the mandate — rather than by the publisher, who is not bound by the mandate, and indeed in conflict of interest with it.
(5) Publishers (partly to protect from rival publisher free-loading, partly to discourage funder mandates, and partly out of simple misunderstanding of network capability) are much more likely to endorse immediate institutional self-archiving than institution-external deposit. This is yet another reason funders should mandate institutional deposit and metadata harvesting instead of direct institution-external deposit.