To me, the difficulty of comparing startups makes asking people to compare two at a time even more important: If comparing AirBnB and Tarsnap is challenging, how can people possibly compare AirBnB and Tarsnap and AutoMicroFarm and Cruise and 14 others at the same time?

I think a bigger problem is what criteria are we supposed to be selecting the startups on? My application wasn't even a startup (just an idea). Should people have voted for it if it was a good idea, if they think I have the track record and resources to build it, if it solves an interesting problem, if it could be a unicorn, if it could raise future investor funds, etc, etc?

Yes, that definitely needs to be clearer. Given the context of "wisdom of the crowd vs. wisdom of YC", I interpreted the sole criterion to be "YC will benefit by making this investment"; it seems that many people took it instead as "who do we want YC to give $20k to", which is a very different question...

The mere fact of who won suggests that you and I were in the minority on this. Most of the problems Dan and Kevin have suffered is due to most people not thinking of what is best for YC.

I agree that we were probably in the minority, but statistically speaking it doesn't immediately follow: Votes for "who do you want YC to give money to" may have been far more concentrated than votes for "who will YC benefit by investing in". I don't know the total number of people who voted; if most people only voted for one or two submissions, then the pinboard-voters would be in the minority.

Only YC knows the answer to this. I would not be surprised to learn that the votes were split into a large pool of people that voted for Pinboard only and another large pool that voted for multiple applications. All I know for sure is they were not voting for mine :)