I haven't eaten at either but we've been inside Cosmic Ray's to get water and weren't really fans of the atmosphere. Our favourite CS in MK is Columbia Harbor House!!
I thought the quality of food, selection and portions were FAR better at Cosmic Rays. The food was very fresh and I preferred their choices.
The burger I had at Pecos Bill was just average. My big gripe however was that the bathroom at Pecos Bill's was the most disgusting I encountered in my entire trip in September. Nuff said.