The comparison between the two is muddied as MSFT and AAPL aren't really the same type of company, even though people try to compare them. On one hand, AAPL has built the most successful retail machine the world has (probably) ever seen and its success over the last decade is due largely to that fact. MSFT is the peddler of the most prolific software in the world.
They're two different animals at this point and from a financial analysis perspective it's perhaps beneficial to think of AAPL as a retail company. I understand that's a very heretic thing to say, but MSFT is much more a pure play software company than AAPL right now.