As mentioned earlier, it's not a problem solely with the Microsoft store, it's a problem that's pervasive in retail in general. I've had some wonderful visits to my local Microsoft store, and some not so wonderful - I guess it just depends on who's on the floor and when.
Similar to the OP, I had an awful time (twice!) at a T-Mobile retail store recently... adding a SIM-only line to my account, I struck up a conversation with the rep and mentioned that I've recently switched to Windows Phone, to which the sales rep replied "Yeah, the 925 is pretty nice, but the 521... terrible, it's just garbage...". Of course, I received a text when the new line was added in the system and I whipped out my 521... the smile from the rep just faded away, and the rest of the transaction went very quietly.
Going back to the same store later to upgrade a family member's phone, a different sales rep had another take on WP... an "Android die-hard, through and through", she talked about how the new iPhone was so great, and how it might make her switch. Asked about Windows Phone, she said that it wasn't for most people, since there's not many apps, and she doesn't recommend it. But that shiny new iPhone... it has such a great camera, and it's so easy to use!!! Of course, my 925 wipes the floor with the iPhone's camera, but you wouldn't be able to tell that in the store - the display 925 had a burned-in display (presumably from being locked on a single demo screen with no attention paid to it) and was locked into the security "death clamp" that blocks the lens. The iPhones are front and center in the displays, with the smaller security tethers and are easy to test out; the only 2 T-Mo Windows Phones are against the back wall, with only a single "This is Lumia" poster behind them, like an afterthought.
I don't frequent Verizon and AT&T stores very often, but I imagine it's more of the same - sales reps are paid to push the product that's more profitable, rarely the product that would work better for the customer. I was in retail sales in a former life - you had the FAB's (features and benefits) that you match to your customer, and always "Show, tell, offer to sell". I believe those methods are extinct now - I've had sales reps actively attempt to talk me out of purchasing something that I've already done my research on. This is why I buy online now.