Berkshire wins by using a formula that relies on them owning whole businesses with sustainable, predictable returns, ensuring that they're extremely well managed, and backstopping them with a gigantic pile of cash that they can use to roll up other smaller bolt-on companies with.
YC works almost exclusively with unproven, highly speculative new firms, with unproven management teams (many of whom will, after joining YC, hire their first employee ever), owns so little equity in each firm that they don't even get a board vote, and by design avoids further capitalizing companies they bet on.
That doesn't make YC bad; the model seems to work extremely well. It just seems like a very different model.
edit: HN->YC. Embarrassing.