I don't know where you got your info from, but Apple Care is great. And I would certainly not buy from a store like CompUSA, Best Buy or Future Shop where they don't know anything about Macs.
I wanted to revive this thread because I've been thinking about this lately. I agree with every point that if I ever wanted the computer serviced for OS or serious hardware issues I would want Apple to have it, I wouldn't want any retail store to touch it. Also, AppleCare has the huge advantage that it covers the OS and main applications associated with it.
Store warranties do have advantages that no one has touched on though:
1. Store warranty covers accidental damage from drops, screen breakage, "acts of god."
2. Store warranty covers battery when it begins to lose its charge.
Being that I work at Best Buy I have a little more leeway to take advantage of these two points, but they are still pretty big deals and other people can really benefit from them. A warranty that covers accidental damage is great because it will hold the value of what you spent. Should the computer incur a serious drop two years after purchased, assuming repair costs are high, you'll receive a credit for the price of what you paid towards a new computer. Thus, essentially holding the value of your computer for the length of the warranty.... that's pretty huge.