Universities have patents for the purpose of selling them, no? If a company is making something and wants to use it, then they buy the patent. No different from today in that case. The only difference is that trolls can't buy the same patents in order to sue others, like IV, Rockstar, and others are doing.

When has a university ever sued someone? Patents generally end up being bought by companies using them... Unless shenanigans are at play.

Here's the first result from Google: http://www.cmu.edu/patent-lawsuit/ CMU vs Marvell.

Here's an article from Stanford law school: 'Are universities the new patent trolls?' http://papers.ssrn.com/sol3/papers.cfm?abstract_id=980776

Universities often (and unfairly IMHO) claim rights on graduate research precisely to monetize and act as patent gatekeepers.