When I go betta hunting I always make sure to take a small flashlight (a penlight works great if you have one) so that I can shine it on the bettas in the cups to get a better look at them. Some stores like PetCo always keep their bettas in blue water that really distorts their colors, but a good bright light helps clear up some consfusion. Even on bettas in clear water cups I find this to be a great help, as they often end up looking quite different under some real light. It's turned a few rather ugly looking bettas into some rather nice lookers xD
The murky greens and browns are closer to a wild betta's natural color, as they weren't always fully irridescent blues and reds, but really, unless one is looking at a wild caught fish or a plakat that's breed for fighting or is only a generation or two removed from the wild, they could at least try to breed some cleaner lines.
I don't think inbreeding is totally bad in bettas, since we would never have developed all the different tail types like Crowntails and Halfmoons, or special color varients like dragons and butterflies if it hadn't been for linebreeding and inbreeding. It's just when it becomes excessive to the point of mutations that harm the betta's ability to function and live that it needs to stop.