Your iPhone is completely covered with your fingerprints. Also, if your phone gets hacked/compromised the attacker could steal the secret used to generate your TOTPs. This is not possible with the Yubikey, it is absolutely impossible to extract the private key.

I have a Yubikey on my keychain (it can easily withstand this), and it takes very little effort to plug it into the USB port when I require it. Less than it would be to take my phone out.

As a side-note, some time ago the Yubikey had a vulnerability with its GPG module so they shipped out new ones for free. I now have the old key (with no GPG keys loaded on it) permanently plugged into my USB hub at my desktop. It is amazingly convenient.

In that case, I might prefer an authenticator to a keyfob that requires insertion too. The yubikey is slightly more secure since it's actually signing a message from the server rather than sending a password that can be (briefly) intercepted and replayed. But it's probably not 'better enough' to encourage someone not to use 2FA at all if U2F isn't convenient.

If user security has taught us anything in the last 20 years, it's that security features have to be convenient or may as well not exist. I think we'll be seeing a lot more 2FA options in the next few years. In this segment, user choice is a huge improvement in and of itself. I've also been testing Duo push for some internal stuff, which is a phone-based experience that's as smooth as silk. To each their own!