Continuing in the trend of 'features I probably should have done at the start of the game but blanked on a good implementation until now':

When you collect a Greenality, the game will automatically save your progress.

When the game loads, it'll prompt you if you want to continue from that number of Greenalities or start a new game.

(Note that WHICH Greenalities you get is tracked, and if you start a new game you won't override your previous save unless you got more Greenalities.)

Hopefully this makes replaying the game more appealing! Good luck on finding all the normal and secret endings!