The ifoAppleStore piece is really rather skewed against Cook. Let's rewind just a bit and recall that the original reason Jobs green lighted the Apple Store concept was because the brand was getting short shrift at the big box stores. There was literally no place in almost the entire world where the Apple-unaware consumer could go to get a true experience of the company's computer products.
Back to 2012, the Apple retail store has matured from a company showcase to a legitimate destination retail business. Where as in 2001 it's purpose was to give consumers a place to expose themselves with Apple's other products, and sales were not the primary focus, in 2012, with multiple locations in every major U.S. metro area, and expanding internationally now, it is conceivable that actual on-site sales takes a stronger focus. Cook has to justify the store's expenses to both the BODs and stockholders (not individual ones like you and me, but institutional holders like mutual & pension funds). It's how all businesses work. Once an element gets too big, it has to pay it's own way. It's why Nike, for example, shuttered so many NikeTowns a few years ago and focused only on the biggest U.S. cities and tourist locations.
Anecdotally, I have not noticed any deleterious changes on the consumer level, at least at the DC area stores. The geniuses have always been "hit or miss," but recently I worked with one of the friendliest, caring ones since I've been visiting Genius Bars (2001). Similarly, recently I went in to buy a Mag 2 to Mag Safe adapter and wanted to try out the Easy Pay app. I had no problem getting someone to show me how it worked (I didn't realize it required location services to be on. Off is my default on every app other than navigation).