It would definitely help if you said more about what your product is. But generally speaking, from the customer's perspective, you should charge for the thing that the customer can predict better up-front, so that it's easier for them to assess your value proposition. You might want to take into account your own costs as well, if applicable.

The interesting thing about Github vs. Bitbucket is that both usage patterns can make sense depending on the project and user. For individuals, you might have a lot of repositories for small projects that end up abandoned after a while. For teams, it might make more sense to have a flexible headcount.