Any issue tracking system is only as good as your ability to act on the information in it. Github issues' apparent simplicity is to your advantage here so I'd stay away from trying to recreate Jira with it.
Kanban boards are a great visualisation tool but the lack of screen real estate limits their effectiveness - more than two screen of information and you end up not being able to see the forest for all the trees in the way. Github projects help a lot with this as you can usually break a project down by structure (modules) or time (milestones). On a given Github board you can easily move cards between projects so the system becomes quite scaleable - within reason.
Kanban boards (if you can keep them manageable) are also a great customer-facing tool. The structure is simple enough to comprehend easily and the customer, product manager, etc. can visualise progress much more easily. They are a great communication tool as they deliver a certain amount of empowerment to the customer.
Checklists are infinitely better for subtasks for similar reasons as the boards - all information and all progress is forced to be on one card - that means it has to be readable and understandable by everyone.
The only limitation I have found with Github issues is that the screen real-estate in the editor is relatively limited. If they had a more complex editor along the lines of Google Docs then it would be possible to achieve the Holy Grail of Issue Tracking where all tickets were well written and had all the information in one place.