One problem I immediately see in this hybrid approach is the requirement to keep the state for all [active] users in memory on the server. This does not scale well - which is why conventional web development tries to be as stateless as possible.
It's not hard to remedy this partly by adding basic lazy-fetching and cursor capabilities to Collection. But you lose some of the most interesting features in the process (push-notify on changes), and preserving those at the same time becomes much more tricky then (bordering on classical ORM problems).
There's also still ground-level stuff missing in Backbone, i.e. the support for recursive updates of nested collections (e.g. from one big, nested json blob) is just not there yet. A few approaches have been discussed, but afaik not implemented yet. The models need to be beefed up with some sort of schema (e.g. json-schema) to truly solve this one.
However, none of that is insurmountable. All it takes is some more of the smartness that the Backbone developers have already demonstrated. And elbow grease.
For example I'd love to see backbone paired with 'dnode' or a similar RPC approach. That might open amazing possibilities.