Please add Yubikey hardware 2-factor authentication to WHM and at the linux root level if possible with some kind of addon package. They have a lot of dev stuff available at Yubikey's site.
U2F as additional 2 Factor Authentication method
It's great that 2FA has been implemented in cPanel version 54. Unfortunately typing over codes is a pain (especially if you first need to find the correct code between the load of other codes I have).
I'd like to suggest an alternative 2FA method: U2F. This is a universal standard adopted by companies like Google, GitHub and Dropbox to provide a faster and more secure 2 factor login experience.
Here's an article explaining the difference between standard 2FA and U2F way better than I ever could: https://blog.flameeyes.eu/2014/10/why-is-u2f-better-than-otp
And on top of being safer, it also looks cool to have to press some shiny button and be magically logged in!