SPOILERS for Undertale
Undertale is a game about determination--the determination to forgive or kill everyone. By giving up, did I lose the game? In a normal RPG, if I had lost to the boss, I could go level up some more, or make some cooler armor, or possibly go do some sidequests and just forget about the final boss. But since Flowey takes away your ability to save (the game goes straight into his fight, and there's no option to run away or defer the fight), it makes the game more frustrating. And while the game's bullet-hell-based combat system is innovative, I suck at it. I don't have the patience or determination to play those kinds of games, so I didn't get to officially exercise mercy or "get" to the end. I think game-wise, I'm okay with that, because boss fights have never been my favorite part of a game.
Control and power and major themes of Undertale. I didn't like the parts where I lost control over what happened to my save file, but it was necessary for the plot. And the best, pacifist ending doesn't give you any levels, which is a way for the player to say, "hey, I care more about seeing what happens if I don't kill anyone than feeling powerful right now." Undertale without leveling is kind of an anti-rpg because there's no satisfaction from seeing arbitrary numbers climb up (so by necessity, combat must be skill-based). The idea that you'll be happiest if you give up power and control over the world is a very religious one (and one that many religions share--Christianity, Zen Buddhism, and Taoism at least). The way the game lets you choose between fighting and "action"ing an enemy feels like the difference between choosing "fight" and "skill" in a JRPG. It doesn't even feel like it will be relevant later on, but it definitely is. Oh, and the way you could actually "flee" the boss fight with Undyne was genius, even though I felt stupid when I had to look it up.
The idea that you have to get to know someone before they'll stop fighting you is an interesting metaphor for relationships--are there some people that you have to put up with some quirks or even abuse before you can really forgive them? The protagonist's passivity in the pacifist route is admirable, but in real life not everyone will change if they encounter someone who is nice to them. But I think the charming and heartfelt part of Undertale is that everyone can and does change in the pacifist route.