The thing is, www prefix was never a requirement. It came about as a convention to very specifically indicate that www.example.com = web server, and ftp.example.com = ftp server, etc. There's no real reason to do it, other than convention from the early days. The CNAME restriction is really the only technical gotcha, and this is slowly becoming a non-issue with DNS services like Route 53 that now allow CNAME on roots.
>There's no real reason to do it, other than convention from the early days. //
It wasn't convention it was that the naked domain wasn't assumed to have web content as not all domains had web servers on them. If you're used to gophering in to balrog.example.com then a www probably was required to get a browser to reach the www pages.
Supposing VR takes off and people have a VR space as their primary internet presence then we might be having the conversation as to why do we both with the vr. subdomain on all the URLs.
The protocol only tells your computer which program and protocol should be used to communicate with the server. The server server name itself is the destination. If you tell your ftp client to connect to ftp://www.example.com it's going to try and connect to the IP address returned by an A lookup to www.example.com. It has no way of knowing you actually want the IP returned by an A query to ftp.example.com.
SRV records could clean this all up, but there seems to be stubborn resistance by web browsers against doing srv lookups.
But, I guess those are more like "old man" companies, not cool new 2016 companies like AirBnB, Uber, and Snapchat. Oh wait, they use www too.