Since the 3DS hardware had a low resolution, use Citra’s "Internal Resolution" setting to scale the game up to 4x (1080p) or higher. Pokémon Y looks stunningly crisp in HD.
Unlocking Kalos: Everything You Need to Know About the Pokémon Y 3DS Decrypted ROM Pokemon Y 3ds Rom Decrypted
Popular emulators like Citra cannot natively "handshake" with encrypted files without specific system keys. Since the 3DS hardware had a low resolution,
To play the decrypted ROM, you'll need a 3DS emulator. The most popular ones are: Pokemon Y 3ds Rom Decrypted