A big problem, THE big problem, is this: http://www.faseb.org/Portals/2/images/opa/Factsheet_Restore-NIH-Funding-Graph1.gif
It's ludicrous to expect public research to work when it is steadily being bled dry of funding. Consider that in addition to the inflation-adjusted losses shown here, there is also the fact that the population is growing and more new researchers are being trained every day. This means more people competing for less grant money.
This is just simple math. Science is fucked because this country, with all of its vaunted interest in scientific advancement, doesn't pay for it. In a situation of scarcity and poverty, all of the results you might expect follow - conservative research, lack of collaboration, hoarding, turf-warring, etc.
The University system and the increasing financialization of universities is also a big issue, but the public funding drought is the main one.
It would be nice if science-heads like the geeks who read this blog were activist about this issue, but essentially no one is. Science can't happen if we don't fund it.