We wanted to use Github at the (small) company I work for, but we have tons of tiny, low-traffic repos. Since Github limits repo count, regardless of how low-resource they are, we flat out cannot use them, period.

Bitbucket has the right idea - number of repos is completely meaningless. Make it unlimited and charge only by meaningful metrics, like user count. Unfortunately, their shift to that plan came too late for us, as we put in the effort of self-hosting. Still, there's that special something Github has that Bitbucket lacks, and we would still consider migrating to Github if only they dropped the arbitrary repo count limit.