The reason I bought it from Gamefly is mainly because the complete packaging will be intact. The condition of the disc itself is questionable, but I imagine it'll be in near perfect condition, they seem to be pretty stringent about that.
Look at a situation I had the other week when I bought a used copy of Fable from EB, the game was scratch-free but the case was a non-standard cheap dvd case, and the instruction manual didn't fit it right.
I know the cases aren't the point of buying games, but I guess I'm a little concerned about the packaging of the games I buy. I'm sure some of you are the same way.