Graduate school was one of my best experiences, and I wouldn't trade my years here for anything. My co-workers were fantastic, and my advisor is golden.
My complaint is with those inefficient bureaucratic systems that you mention in passing. Life's much easier without them. :)
I think there is a big disconnect between industry and academy. When I was a grad student (got a masters in CS) there was a huge lack of problems to solve at school. I went to Sun and after about a year I had 9 fantastic PhD problems.
Be nice if we could fix that. School is great, industry is great, somehow connect them.
Graduate students tend to love to complain as much as possible about things that aren't that bad (I know I was one) and people leaving something idealistic often have a compelling need to try and put it down in any way they can to justify their decision to give up on the idealistic goals and try to make some money -- which is why you see so many "goodbye academia, you are broken" posts and blog entries. And some people have genuinely bad experiences like at any job -- bad manager, particularly low funding, bad co-workers, you're going to have a bad time.
That being said YC research sounds amazing. Basic research was funded by charity from the superwealthy (or only carried out by the independently wealthy) for most of human history, the model works. Researchers tend not to look into areas or find results which are bad for their backers. It's good to have some public and some private sector; we need to balance out the conflict of interest a bit.