Sherri,
Bottom line is that shipping is hard on fish, period, so no matter what we do, it's not an easy thing to go from bag to tank. We've had out share of losses, trust me.
That "rough" look can mean a lot of things, or a combination of many: coloration (bright, pale?), fin condition (not always, as lions do come in with torn/unsheathed fins that heal up just fine), more importantly how they hold their fins (are they extended? clamped?), the look of their eyes (beyond cloudiness or clarity)...think of someone who isn't feeling well, how their eyes just seem "off". Body mass, shape and "blemishes" also help determine the fish's condition. Of course, you can't observe the fish eat or swim from an etailer, so you're limited to what you can see in a photo.
Those are the "tangible" things, but after awhile, you get a "sixth sense" about a fish where you can look at it and think "that fish ain't doing so well". Renee has an uncanny knack for this (maybe it's her years as a nurse), but she's almost always right. In fact, at work, some of the girls are a bit superstitious (for lack of a better word) about her because she can do this with patients.
Lisa,
Your experience with the bluefins is similar to ours...they seem to come down with a raging bacterial infection that, as you've seen, basically comes on overnight and the fish literally "fall apart" (we had one that had its jaw melt off). Our specimen that we've had over a year now has undergone at least two, maybe three courses of oral antibiotics when we've seen the tiniest spot on its pectorals, and it has seemed to do the trick (besides keeping it at 63*F max). IME, these fish are the touchiest of the touchy, as even tho they eat well, they're very non-aggressive feeders.
All we can do is keep learning from our experiences and each other...