There are two yarn stores near me now. One isn't very convenient--it's between my office and home, really too far to go on a lunch hour, and it's usually closed by the time I head home, and too far for me to want to drive there on the weekends. The other one is closer to home, and a nice convenient location for visiting on the weekends. They have a lot of inventory, and they carry Noro yarns, which is like crack to me.
But they arrange the yarn by color, which drives me nuts.
It may make a nicer presentation, i.e., more dramatic or something, but it's almost impossible to find something, even when you know exactly what you want. Maybe that's the point, maybe it's more conducive to browsing or something, but it mostly just annoys me.
I remember being in there one Saturday a few weeks ago; I had gone in for a skein of Kureyon. I searched and searched and searched, and finally found it, and as I was walking up to the counter to pay, another customer stopped me and asked, "Where did you get that??" She and one of the women who work there had been searching in vain for it. It was multicolored, with turqoise and grays, and they had been looking in the blues. I pointed to the other side of the store: "It's over there, with the grays."
I've noticed that one color of Noro Transitions (and probably other yarns, too, that's just the one I noticed) will be all over the store--if you wanted enough for a sweater, you'd have to go around and collect it from every corner--since the skeins are multicolored, some would be with the pinks, some with the browns, some with the grays, etc.
I know there are a lot of different ways to arrange inventory, but it would seem to me to make a lot more sense to have one kind of yarn together, to have all of the, for instance, Noro Silk Garden, in one place so you could compare different colorways without having to carry an armful of it over to the other side of the store. But maybe that's just me.