Better filters for emails. Would love to subscribe to only new issues on a repo or random issues on a repo. Basically http://codetriage.com
I follow a couple dozen projects and after a couple days, my GH notifications page gets insane. Making issues more usable would be a big win imho.
Also, a "priority" follows would be nice too.. so your org/project issues can be viewed separately from your follows. Seeing adoption of something closer to ontime/tfs/jira would be nice too.