This is the cunundrum:
The local quilt shop (LQS) -- the fabric is top quality, the prices reflect that, the manager and employees know what they and you are talking about, they are generally creative thinkers who are loaded with information, and they give encouragement and feedback about your ideas and efforts. Hit the store at the right time, and you can feel as if you're in a workshop especially designed for you and your current project.
JoAnn's and other "big box" stores: you search and scrounge, the bins / hooks are empty, the employees don't know anything about what they're doing, they act like drones, you and your questions / concerns are not their problem (if not theirs, then whose???), and they have no clue as to what the price is of anything. Math and English are both foreign landguages. The stores try to incorporate all the various crafts (sewing, quilting, scrapbooking, flower arranging, beading, jewelry making, cake decorating, etc.) into one store. The psychology of that is to keep you in the store as long as possible so that you will leave more of your dollars with them...it falls under "browsing" and "impulse buying".
So, aside from the obvious differences (see above), the primary difference between the two places to shop is summed up in one word. Local. JoAnn's isn't and your quilt shop is.
The local quilt shop has "skin in the game", its survival depends on your repeat purchases, its survival depends on that very tenuous commodity called "good will" (hard to win, easy to lose), its survival depends its relationship with YOU.
JoAnn's and ALL the big box stores don't have to that mind set because there will always be someone behind you willing to put up with their no customer service.
America, with its pop culture of use it, toss it, get another at the cheapest price possible, is learning the lesson of what it really costs to by-pass "local" for "big box convenience". America, you're getting what you've paid for...not much. "Not much" is very expensive, especially when you consider the number of jobs and dollars that are no longer "local". That covers everything from the Dollar Store to General Motors.
Just saying...