We love Github Issues at our company, but it's missing one thing we really need: metrics. We need to track when a milestone was started, who completed how many issues in a milestone, what was the issue estimated at and what was to actual time to complete. We need data on what there is to be done and what will be done.

That being said, I don't think this is a feature set for Github issues. This is not an open source concern; it's a business concern and I don't think business should drive Github.

So a third party integration is perfect for this. Is this something on the roadmap of waffle.io?

Yep. We're definitely looking at adding more planning functionality and metrics around milestones in the near future.