We use Zenhub with Github issues. Zenhub adds more structure over Github project. It hit the sweet spot for small teams, not too basic where we can't use it to run our processes, yet not so bloated where we need a manual for doing things. The tight integration with Github is a big win for us. But you can't customise things so when the team gets bigger we expect to move.
https://www.zenhub.com/