Trying to integrate Jenkins w/ Github Enterprise proved to be a real pain for me. It wasn't clear what git* plugin is the best to use for how I wanted to setup builds. It's literally impossible to deploy Jenkins in a repeatable manner with just configuration files, you must get it online and use the api to configure such simple things as API keys (eg, specify the ID of the key so your jobs actually reference the key and don't break).

Another big pain point, for me was, no obvious openstack integration. I wanted my jobs to run on ephemeral instances so all my dependencies could be defined in the job themselves, not having to rely that the Jenkins worker is setup just right.

I think Gitlab runners get this right, but I have not investigated too far.