This is a great post on a topic that is quite close to our hearts since we are a science-startup as well. I think that this situation is a symptom of the mentality, 'You can't be fired for buying IBM.' It is so much easier to give money to a research group at Harvard etc than 2 guys starting out from an apartment. Especially in a bureaucratic setting where your job is to make decisions that do not look bad, and not to actually make good decisions!
Adam and I were once on a call with an academic consortium that had received ~$15M in funding from ARAA. The objective of this group was quite similar to what we are doing with our startup. This group reached out to us too see if there was a way we could work together. During the conference call it was Adam and me on our side and at least 10 researchers from institutions all over the US on the other side!
Those were the early days of our startup and we thought that we would be obliterated by them with their vast resources. It turns out that with 1/10th their funding we have done more than 10x of what they did. And they are floundering while we are just warming up.