Disagree somewhat with eye, more certainly with base running.
You learn base running, and the more experience you have reading a pitcher, they better you are at it. The "processing" part is speed, not the ability to read a pitcher.
Eye, it's a toss up. Again, the more pitches you see, the better you are at recognizing a pitch and what it's going to do. The physical skill needed to process that, is it eye, or contact?