As an example you talk about needing a special device to manage keys which presents problems. It centralises your identity to your yubi key (instead of email), lose your yubi key and you lose your identity, what if it gets wet, crushed, corrupted, your fucked. Instead we encrypt the key and distribute it across the net, if a copy is deleted or corrupted there are other copies and its available to you anywhere anytime. Currently your identity is centralised to your email, if your email goes down you lose your identity, if its distributed and a copy goes down you just use it like normal.
Distribution solves pretty much all the problems centralisation creates, its just really complicated so we generally don't bother.