Where to stay? Pros/Cons?

I cannot speak for Anacapri but spent the day in Capri a few years ago. It was beautiful and the highlight of my Mediterranean cruise.

http://www.fodors.com/community/euro...l-opinions.cfm

Anacapri is located much higher. You can take a chair list to Mount Solaro for an even more breathtaking view.
Why both are touristy, Capri feels more so. Capri also has an upscale area. There are more ways to get to Capri from the Marina Grande.

Without reading the link that ekscrunchy helpfully provided, I don't think you have a bad choice, but would say that Anacapri is likely to be more laid back and Capri more up-scale. Depending on how long you plan to spend on the island, you might want to consider how easy / difficult it would be to see / experience the things that draw you to Capri.