I didnt get it to production state, as my team setteled with firestore as we need a database as a service with low cost at that time. So nothing to point out from my own experience with graphcool
But I think graphcool limitations would be the expected limitations of postqresql and mysql in general, as graphcool is still built over a postqresql database.
Still right now there is no easy way of deploying your own grapql api other than using graphcool.
I hope that was useful.