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According to my understanding of this document, Yubikey is capable of running ed25519-sk and gpg-agent.

Which one is more secure? Obviously, ed25519-sk wouldn't work, if the SSH server is old, but other than that, is there any downside of using ed25519-sk vs. gpg-agent?

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As of 2022, you should prefer Ed25519 wherever possible.

The only scenarios where other signature algorithms might be preferred over Ed25519 are:

  • You are legally or contractually prohibited from using Ed25519, e.g. for regulatory reasons (like FIPS).
  • The systems you need to interact with do not support Ed25519.

If you'd like a more in-depth evaluation of the options, I recommend Soatok's guide to digital signature algorithms (2020) and guidance for elliptic curve signature algorithms (2022).

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    Sep 11, 2022 at 18:32

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