Which Cryptographic Standard ensures cryptographic agility and good adapotion
All but NaCl allow you to specify algorithms, but none of them would allow you to specify an algorithm that is part of the Post Quantum Cryptography initiatives yet (which, although unmentioned in the question, would be a very good reason to have crypto-agility).
For classic cryptography and a relatively high resistance against quantum computers, all those allow for RSA key encapsulation (including RSA-OAEP) and 256 bit AES as primitives. So using an RSA key pair of, say 4096 bits, will allow you to have a pretty good resistance against anything but a full featured quantum computer with more than 8192 logical qubits.
Otherwise I'd make sure that I would use a standard that is practical for you, that has a mature, well maintained library and is checked for e.g. side channel attacks. That's also something that's a good property of CMS; it may be old, but there is little wrong with maturity when it comes to choosing a library.