What requirements would lead to the development of a new security protocol? I recently completed a semester studying some basic amount of cryptography. So my knowledge is not very broad/deep. 

What I currently see is that we have a bunch of fairly secure encryption modes to encrypt data and fairly secure authentication protocols to authenticate/identify subjects.

Now security protocols are a broad domain. Sticking to encrypting data and authenticating users, are there any use cases (ability to process encrypted data or special authentication case, if any) that the current set of well known protocols  don't cover? Do industry researchers need to spend time coming up with their own protocols?
There are plenty of security issues which are not yet solved with widely used protocols:


At the low level there are reflection/amplification attacks. DNS (and in particular DNSSEC) is known to be vulnerable to this. DNS cookies have only recently been standardized, and is not yet widely deployed. Other protocols are lacking in this area as well.
Logins are still performed in ways that allow servers to see passwords in clear. Rather than fixing this at the protocol layer we have tried to educate users to use different passwords for all sites. It is still a possibility that improvements in this area may become popular.
Anonymity is not very well protected by current protocols. At the moment there are big players actively trying to undermine users' anonymity. New protocols might try to address this.
Confidentiality could be protected better with opportunistic encryption. Opportunistic encryption where identification of the peer being communicated with is optional can improve security compared to a setting in which communication is done unencrypted due to the complexities of key management.