Very cool! Some simple feature ideas:

It'd be interesting to be able to use size or color to indicate additional dimension(s). I like to measure “return” in terms of impact/urgency and “investment” in terms of cost/complexity, and then maximize “ROI” instead of just maximizing “return”.

The ability to sequence things seems to be the biggest thing you lose with the no-list representation, but I think that's easy to fix: let the user add “edges” between “nodes” to indicate dependencies.