Initially, I also thought New York City would be a much better choice for a Golden League meet when compared to Eugene. The bright lights of the big city would be great for the sport and the amount of marketing potential for the event is huge, especially if top stars like Usain Bolt, Tyson Gay and Jeremy Wariner took part. However, the IAAF is going to go choose the events which they think will have the biggest draw and have the best organization, and the top U.S. event is the Pre Classic.
My comparison for this is with NASCAR. I've never watched a single NASCAR race, but I'd compare the Pre Classic with the Daytona 500. Daytona Beach is not a large city, it's not even a city. Daytona Beach has a population around 65,000, not even half the population of Eugene. Yet every year the Daytona 500 is the most anticipated, most watched NASCAR event in the country, and one of the most watched sporting events of the year.
The Pre Classic is like that. It isn't hosted in a big city, and it is way out of the way if you are trying to travel there, but every year it is considered the top event in the United States, and is one of the top events in the world. If the IAAF wants to include the best meets in the Golden League the Pre Classic is the best the U.S. has to offer, thus it should be the American representative.