There seems to be an issue with save/load affecting the endings. On my first playthrough I saved before the choice and got ending 1, and on my second playthrough I loaded up the old save to choose the other option and got ending 1 again. I then did new playthroughs from the start, and got ending 3, 4, and 5 without ever getting ending 2. Had to reset the game and play without save/loading to see it.
But other than that, it was a great game. Interesting story and nice use of persistent data.