- Backup is per-website. Every new registration requires you to e.g. print a slip of paper and store it in your safe/friend's house/secret drawer.
- Each website has to implement their own backup flow. That's extra cost, hurts adoption, and some don't even bother with that.
- The PIN is extremely low-entropy, which requires absolutely perfect rate-limiting. As soon as the attacker is able to side-step the rate-limiting (which has a large surface area), the OTP is useless.
- The PIN is vulnerable to shoulder-surfing and surveillance. Can you type the PIN faster than the attacker that's using OCR?
- Typing a PIN number (that has a timer!) adds friction and mental angst.
- And I may be wrong, but as I understand all devices have the same level of trust. If your phone is stolen, it's a race to revoke the thief's codes before they revoke yours. Ideally you should have some "master secret" in your safe/friend's house/secret drawer, that is able to revoke any and all devices because it's the safest secret you have.
- It's only suitable as a second factor, not primary. You are probably also using passwords, which adds a whole lot more security and usability problems.