Honest answer: Because I want to focus on distributing software rather than a generic "one size fits all" (no one) upload anything model. It wasn't a good solution. S3 is a better solution.

Uploads may be going away, but the functionality behind it is being focused in a more usable, elegant way. Case in point: image attachments (the primary use for our uploads section until Friday). Which has all of the legal and support ramifications of the old Uploads section.