Excellent game.
Just a few more tweaks to the engine, and it'll be perfect.
First off, give the player the option to remap their path, without needing to die and go through the cutscene again. Second, if the player dies, give the option to change node placement without remapping their path. Third (though this would require a lot more effort than the first two), instead of simply saving upgrades but not unspent AP, record the AP high score for each stage and at which stages the upgrades were bought.