Ember Data can be really powerful, but is even far worse in the "black box of magic" department than Ember itself. There's a lot of crazy internal state and logic being fired off in all directions, and it can lead to very strange state errors and race conditions.
I'm really glad to hear that they're adding an adapter type that can be more powerful than just an $.ajax call while not being quite as complex. It was by far my biggest complaint with Ember.
(of course, I hope this doesn't stifle development of more full-featured adapters - I think half my problems with Ember Data come from the LocalStorage adapter I'm using having some major issues ;p)