We understand that cleaning/filtering/preparation are key to the analysis, and we plan to support those operations as part of package construction. The question is whether or not that work should be done repeatedly, or once for the benefit of your collaborators.
You can store any kind of data in Quilt. Not just data frames. What's on Quilt today is just the beginning of what is possible.
Do you also dislike GitHub? We've opened up the client source and the community for as much free data as people can publish. It seems naive to expect that we wouldn't charge for anything ever. The users always and forever control their own data, by the way.