I'm going to be doing a pretty big comparison later this month, as I will be buying a new set of speakers. I'm considering six or seven different models. Only way I can do this, as best as possible, is lug around my amp and CD player to each store and listen through those. Really, I think whichever speaker moves me most, and doesn't offend in some way (e.g. is too bright) will be the one I end up with. I'm going to try going in with no preconceived notions as to which speaker will sound which way, and to not over-think things. I'll bring my own music that will allow me to test bass, treble, and just how involving, detailed, and musical each speaker sounds.
This won't eliminate all variables, but should eliminate most of them. Especially when comparing two models in the same store. You are in the same room with the same electronics powering the speakers. So whichever speaker sound best is really the one to choose over the other one. The only concern after that is the room, but unless you can do an in home trial you'll never get around that.