To understand why, I recommend you have a play with them yourself. It is immediately clear, in my opinion, that Graph.cool is a much better designed product in every aspect. Graph.cool's UX exudes refinement and quality that Scaphold's does not.
An example of this is the fact they invite you to their Slack team automatically when you sign up (i.e. use the email you sign up with to invite you, you don't have to do anything). They really care about their customers, and the Slack community around Graph.cool is much more active than Scaphold's. In fact, it's mostly the community that is buzzing around on Slack, and it's about people learning GraphQL, not necessarily learning how to use Graph.cool. The Graph.cool team seem to be really motivated to help everyone learn to use GraphQL, not just their service. This is also evident if you get in touch with the founders of Graph.cool - they are just nice people to talk to.
Any feature distinction that Scaphold may have over Graph.cool is quickly disappearing. I can only think of one, subscriptions, and Graph.cool has that on their roadmap to be released very shortly. On the other hand, Graph.cool has plenty of features that Scaphold does not, such as Auth0 integration, Relay AND Apollo support (from the same schema), a much better permission model.
Oh, and it's free (for now) :)