I absolutely agree. It's a pretty core piece of Undertale's story though, so I wonder how it can be executed in other games without feeling like it's just an Undertale rip-off?
Use other limitations and quirks of the medium. They haven't all been explored in depth yet. Imagine a game where having state-saves like in emulators would be a feature of the game that it fully embraces for an example, and you'd end up living in several versions of the same world at the same time to fully beat the game. It would be like saving just before making the imperial/stormcloak choice in skyrim, but then as you switch saves the game actually acknowledges that and is influenced by it. It could be a really cool concept if done well, and there are many more such quirks for people to take advantage of.