The main thing I notice is thread count. Some of those Joann's calicoes are so thinly threaded, they're almost like a screen! But not all Joann's calicoes are made equally, I've found nice heavy thick fabric with the "made for Joann's" label too.
I haven't noticed a difference in fading, but I am really careful to keep things out of the sun so I haven't had much fading of anything at all.