I do not think the problem is with how many options we are presented with, but rather with the difficulty of figuring out what primitives are actually needed to solve a particular problem, and how to compose those primitives. Do you need digital signatures? Do you need a hash function? Do you need to establish a common random string before the system can be used? It is very easy to assemble a system that appears secure (it's encrypted and signed!) but that does not actually provide any meaningful security (oh no, we actually needed non-malleable commitments!).

A high-level language could help quite a bit, because it would help programmers abstractly specify the needs of the system rather than getting lost in the details of which operations to choose. Maybe you really only need to sign and encrypt your messages. Maybe you need to sign, encrypt, then sign again. Maybe you do not need signatures at all, but you need to use a non-malleable cipher and a few rounds of communication (e.g. to make a deniable authentication protocol). The next generation of security problems will not be solved by slapping on encryption and digital signatures; we are going to need to pay increasing attention to higher-level issues.