- Attachments in the issue tracker. Pictures tell a thousand words and it would be infinitely easier for user submitted issues to have screenshots.
- Better code search.
- More granularity in the notifications. For instance, I'd love the ability to toggle email for my own repos but leave it to web notifications for my watches. I've missed pull requests because of the deluge of messages.
- Better reliability.
It's a great tool. I really enjoy using it, but with a few additions it would be near perfect.