Transistor was lovely. The mutability of the combat and the evolution of the story were complex but worthwhile. Two amazing moments stick out (spoilers):
When you find the boss has committed suicide with his lover, distraught over the damage he created. Just a powerful and sympathetic end to a character that doesn't require a fight
When you realize that your enemy can now stop time and attack you without you being able to do anything. That reversal in the final fight killed me instantly the first time and I loved the powerlessness and requirement of mastery it provoked. I had to be really efficient with my tools and attacks in and movement in order to win.
Transistor was great!
(Also, also, as others have said, requiring the player to experiment with weapons and powers in order to unlock story that builds the world was a clever synergy that many games should copy).