I am a quilt store owner replying
The best quality fabric comes from Japan and South Korea, not China, Pakistan or India. Your LQS normally purchase from Japan and South Korea where the fabric is much better woven, both tighter and thicker, the prints are clearer and the metallic fabric is awesome. South Korea and Japan, first world countries with higher labor costs, have higher standards for their fabrics, so I know that anything purchased from those countries will be exceptional.
The manufactures that sell to the LQS, generally don't sell to Joannes. There is one manufacturer that does, except that the fabric sold to Joannes is printed in China and the good stuff sold to LQS is made in South Korea, thus there is a price and quality difference.
The real question that I see is this... You are making a quilt with love for someone. You have spent 20 to 60 hours working on that quilt and alot of people spend the money to have a quilt, quilted for them. So, why have you spent all that time, then spent the money to have it quilted, to end up with a finished quilt made of inferior fabric?
The other issue is of course customer service. If you come into my store, you will get personal help. If you need help with a technique, we give it. If you have problems choosing fabric or colors, we will bring fabric to you that will go together for you to choose from. We have a classroom that you can sew in free of charge and bring a bunch of buddies to sew together. We have classes. Get stuck on a project, we will help you out. Want a demo of anything in the store, we give it. We can custom print fabric, so bring in your pictures and designs. Want to brag and show off what you have done, we would love to see it.
So these are the differences between the chain stores and the LQS. Yes, some LQS need lessons in friendliness and helpfulness. I just hope that all LQS will demonstrate the love that we have quilting.
Meredith, Beautifulquiltfabric.com, Beautiful Quilt Fabric, San Dimas, California