We think PFFile is a lot easier to use from mobile devices, with the iOS and Android SDKs. A lot of people are actually just using PFFile because they find it simpler than using S3. That said, you can use S3 and Parse in the same application, so they work together fine if you'd rather implement things that way.

I'm currently using Parse for data and S3 for file storage. I will give it a try to PFFile in another project to see how it works.