One thing I really like about a web technology-based interface is the idea that maybe the computer running Pd and the computer accessing the interface wouldn't necessarily have to be the same computer.
I'm imagining running Pd on a small single-board computer, and patching/interacting with it on a tablet or a phone or a laptop, connecting over an ad-hoc wireless network.
Node-webkit from my understanding is really only intended to run locally, as if it were a native application. It includes an implementation of a web browser so that it can run, and that is where the ~100MB bloat comes from.
Maybe instead of relying on node-webkit we could write our own tiny node server, and have users jump into their favorite web browsers to access the interface?