Clearwire setup and Sprint Network Vision setup are completely different. Sprint was going to use the network vision work to set up Lightsquared's network for them, but they are dead in the water. Clearwire will still be up and running in those cities until 2015.
As far as which cities Sprint is picking for Network Vision... I'm sure they have a reason for it, maybe they are tackling the biggest cities first so they can boost phone coverage. I know that Network Vision looks like it is purely data, but in this day, people will not tolerate dropped calls, so they need to bolster capacity and dead spots to keep customers.
And it is obvious that Wimax no longer sells. It has been downgraded in customer eyes to being in a class with HSPA+ and although T-Mobile is throttled, it is still unlimited. Sprint needs LTE up and running in the big cities to draw customers.
From what I have seen so far, Sprint's buildout of Network Vision buildout makes a heck of a lot more sense than Clearwire's.