Case in point A: Skype leveraged an initial P2P design at a time where direct addressability was the norm (and there were many freeware alternatives that allowed direct dialing)... Now that Skype has become dominant, it has switched to a centralized infrastructure 1) because it's owners can (it makes administration, censorship, and surveillance easiest), and 2) because a P2P model no longer makes sense with most users relying on their centralized bootstrap servers.
Case in point B: Dropbox and similar services have replaced self-hosted FTP, I would argue, simply because noone wants to maintain static port mappings and Dropbox is easier.
Even without other incentives, the presence of NAT is a centralizing force that - taken to the extreme (such as with carrier NAT) outright precludes P2P - and that is undesirable. In an Internet with NAT (or any other violation of the end-to-end principal) all systems suffer the same fate: centralization (the antithesis of P2P).