If I were a betting man (well, I am) I would say the main reason Jones is in the slot over Naaman, Roscoe, or anyone else, is that they love his ability to block. It's no secret that they were trying to get Nelson up to speed on blocking this summer and use his size to put him as a bit of a tight end type to get mismatches. In fact, that's how he got injured early in camp, in blocking drills.
So, on top of the fact that they love Jones blocking and the fact that he knows the entire playbook, the others simply can't do what the Bills expect out of their "slot" receiver, which as Pat Kirwan gushed about during TC, is actually more of a second TE than your every day definition of a "slot" receiver. Think David Nelson, not Wes Welker and definitely not Naaman.