This is the way I see it....
If something doesn't fit correctly and you need to return it and it is pretty much still brand new, no big deal....the 90 day return policy is to show the consumer that they are willing to work with you....if you buy a shoe and it falls apart within 90 days and you aren't excessively running/walking in it (like it has 100 miles on it), you should return it because that would be unacceptable.
I have done this with Road Runner Sports as they have a similar policy. I bought a pair of trainers once and after less than 150 miles the tread was completely worn to the point of being smooth...I explained to them what happened and exchanged them, no problem.
These issues shouldn't occur much at all; especially if you find a shoe you like and keep buying the same model. Same with clothing once you know your size.