There are certainly areas that github could use some improvement. One of the basic features that I see as currently missing is actual side-by-side Diffs like those available in Chromium Code Reviews[1]. This makes it so much easier to review code changes and thus improves the experience of collaboratively working on a project. The Github folks are smart people, so I'm sure they know this and yet years after launch this is still not available in Github while they continue adding things like improved map diffs [2] which while nice features on their own, it only serves to show that a good code diff experience is not as important to them now.
Secondly, I find Github search to be lacking in terms of fulfilling its potential. It seems we all agree that Github is the number one place most people put their public code on. This is great, we have one central public repository. And yet searching for, finding and discovering good code on Github is not as easy as it should be. I argue that it should be easy to find solutions to programming problems that others have already tackled. Imagine being able to type "compute sha256, c++" and seeing relevant code snippets right there. I am not saying this is an easy problem to solve, but I think it's definitely worthwhile one to try. Who knows, may be someone will build an awesome code search engine on top of github.
[1] - https://codereview.chromium.org/261573002/diff/60001/google_...
[2] - https://github.com/blog/1772-diffable-more-customizable-maps