From an older thread, this was my take on it:
For me personally, I chose Best Buy over Microsoft this time in respect to the loyalty/rewards program that Best Buy offers. Not sure if you know about the details, but you essentially get a percent of your purchase back in certificates that you can use on just about anything when you earn at least $5 worth of points. In the upper tiers, you can opt to save your points up for when you want to use them, and this is one thing I really like. I'm currently sitting on a little over $200 worth of points. For the higher tiers of membership, you also need to spend a certain amount per year. Best Buy just changed the tier structure a bit, and the highest is $3,500 spent annually. The SP2 can help towards that number.
Warranty-wise, I think I've read on here that some have bought the Surface Complete (or whatever it was called) from Microsoft even if the tablet itself wasn't bought from them. Also, as others have pointed out, you can use a credit card you have to take advantage of extended warranties, purchase protections, and even double-dip on loyalty points through the card.
My RT and SP1 were bought from Microsoft for the "support your local businesses" approach, but I needed about $1,800 more to maintain my tier on Best Buy and I do like the points program.
And any issues I had with my Surfaces bought from Best Buy were handled by Microsoft, either at the store or with customer support. I think this option works pretty well.