i understand what you mean about the resale shops being difficult for taking orders... every time i'm going to japan i got like huge shopping lists from friends with me and it's almost impossible to track down exactly what they want... half of the stuff is out of stock, the other half only trackable in bits and pieces... it's tiring. :/
BUT! nothing cooler than browsing through the stores oneself - i always end up spending sooo much money in the ikebukuro and nakano mandarakes, omg. and not to forget the ikebukuro animate... imho it's best to climb all the way to the top right in the beginning and then work your way down (and usually end up with 3 or 4 bags, urgh) XD