Actually, things are running pretty smooth for months now - see for yourself at: https://status.github.com/graphs/past_month. If that's not your experience, you can reach out to support@github.com and we'll look into it.
S3 has 9 9s of durability and is "closer" to where our servers run so there are less possible points of failure. We have had 0 issues since migrating to s3 backed git repo 2 years ago.
We still use github for day-to-day scm mgmt as you guys have tons of extra value add.