Isomorphic apps are the next big challenge. Right now the biggest blocker is that everything's a singleton. I'm working on an internal container which should hopefully mean existing apps can be made isomoprhic without a change to the API
I've found that contexts are a good way to handle this - they're basically invisible props that get implicitly passed down the component tree, and mixins can whitelist which parts of the context they want to be able to use. They're undocumented, but they're used quite widely in React, so I doubt they're going anywhere. You can have a top-level component instantiate new dispatchers and stores and expose them as i.e. "this.context.userStore", "this.context.dispatcher" to mixins and component code. And this can be done concurrently in the same Node process without needing VMs/sandboxing. Your state mixin API might need to change a bit, but it can be substantially the same:
var UserState = Marty.createStateMixin({
listenTo: "UserStore",
getState: function (UserStore) {
return {
users: UserStore.getAll()
};
}
});