The thing I'd like to see Github focus on with their API is granular permissions. There are many SASS integrations that I am just not comfortable with granting access to because I don't want to have any more than necessary 3rd parties having access to repositories. Please correct me if I'm wrong, but every time I grant an application access to my Github account, it automatically has access to all repositories I have access to. I know there are ways that organizations can set permissions such that they can approve app integrations. Still, there are private repositories I have that I would prefer to not have 3rd party integrations be able to access. With 3rd party SASS providers having access to private repositories, it would be trivial for code to be stolen or sold to competitors. If they wanted to be real nasty they could rebase and force push, delete branches, tags, inject malicious code. There are so many potential ways that providing full access to everything you have access to in Github could be exploited.
I would love to see Github add permissions to apps requesting OAuth permissions be able to restrict access to the repositories the 3rd party app has access to. It would also be nice to be able to revoke individual permissions.
[Edit] fixed some grammatical errors.