I don't mean this in a negative way either, but what do you think it is that set this game apart from the rest? It is the style? The themes? The plot and writing?
I think it's likely a combination of multiple elements, but I think one of the most important things are the secrets. A lot of modern developers (especially AAA) avoid creating too much content that players might miss, for fear of spending their money on things that might not even get seen by players. Undertale took the opposite approach, and fill the game with so many secrets that there's even a Reddit group dedicated to data mining the code to find more secrets.
What does everyone else think?