Well done.
You did a good job in creating both a retro and a scary atmosphere.
Forcing the player to ignore Twilight's advice as well as putting them off guard with the initial friendliness of Sunny Town was achieved beautifully.
Odd, maybe, but the part that managed to scare me most was when you enter the mansion and there's some "dialogue". The empty dialogue boxes had an unnerving effect, because they don't influence the game so much as they influence my understanding of it. Messing with the player's head, to make them feel as lost as the in-game character, that is the key to scaring them.
From there on out, I'm afraid the 'freak out' factor decreased somewhat. Sure, the ruined town had a spooky atmosphere, but the music was a bit too present in my opinion. Certain parts of it fit well, but others were too active. Most of the dialogue was only moderately unsettling. It came off as just a tad stereotypical 'city of crazy people' dialogue. "She was going to ruin the party", "We'll never let you end up like her", "Stay with us"... it's by no means bad, but next time, I'd advise dialogue that's a little less predictable for the situation. Involve the player emotionally. I hope I haven't stopped making sense yet.
Now, back to the positives. Making one of the "silhouettes" just stand there was clever. It makes the player ponder if they should come near them. The third silhouette to appear moves in incredibly unsettling spurts which sent a bit of a shiver down my spine.
The role of Ruby in the whole thing is interesting, but hardly elaborated on. Can we expect a sequel?
Ah, that turned out to be quite a rant. If I came off as negative, I didn't intend to. You did very well, and I hope to see an even more unsettling sequel. I hope my critique is somehow useful.