This is focused on the researcher world, but the arguments hold for other fields
Q: What is the primary factor for ranking researchers?
Surely the aim, therefor, of the researcher is to market her work as widely as possible, to maximise the potential for citation.
Given that we are now in the Information Age, where The Internet is the primary source of answers (backed up by reading what has been found, on paper), then the sensible solution is to place enough of the research results on the Internet such that they can be found and assesed, and followed up.
Where, in the Internet, this material is placed is almost moot: the Internet has no location per sae - Search Engine index everything, everywhere.
Q: What is the primary factor for ranking Institutions?
A: The amount of research performed by researchers of standing (see above)
Surely the aim, therefor, of the Institution is to market the work of their researchers, with sufficient "corporate identity" attached, as widely as possible, to maximise the readership of that work.
I think we can say that researchers need publicity, and Institutions want to be the ones to do it.
The question I see is:
"How can we make it easist for the researcher to publicise their work, and how can we help the Institution capitalise on that individual publicity?"
"Institutional Repositories" are the current solution - are they the right one?