In doing product management on an engineering-led project, GitHub Issues rock. The killer features are that it’s a) really simple, b) tightly integrated with code (you can reference/close issues via commit messages), and c) facilitates discussion of issues just like it does of code.
What GitHub Issues suck at is being able to get a high-level view, where you can see more than 30 issues at a time, and broken out by milestone or by person. (You can only filter to see issues for one milestone or one person, but not easily move multiple issues between them.)
I’d really like to see a Trello-style interface for managing GitHub Issues. Some very limited integrations exist, but what I’m looking for would let you quickly move issues around between milestones. This would help plan a product roadmap and be able to visualize what the upcoming milestones look like in one place.