My thoughts are that, as companies became larger, they calcify and innovation ceases. Graham mentions Detroit in passing in that article but doesn't acknowledge that, in the 1910s Detroit WAS a hub where enormous innovation was taking place. I want to ask: where did Detroit's nerds go? The region still is quite wealthy[0] and has more millionaires than San Jose. However Detroit has neither an intact urban core, nor a flagship university. The auto industry barons (like Henry Ford or Walter Chrysler) never built a namesake college, the reason for that I'm not really sure.
Graham also mentions Pittsburgh in the article. As a native of the city I think he discounts the changes that have taken place in the decades since he has lived here. There is definitely an interesting old urban city here with a reasonable sized start-up scene. The winter weather is no worse than a place like Boston. He's right about the lack of VC wealth, though. It seems that all the old steel money isn't really interested that much in funding tech start-ups, although I think that's slowly changing too.
[0]http://247wallst.com/2011/07/13/the-american-cities-with-the...
The best article written on the difficulties of becoming the next silicon valley.
Keep trying....stay hungry