Cognito is for authenticating users while AWS SSO is for authenticating employees. Users don’t usually need to be stored in Active Directory, authenticate to other services with SAML, or assigned groups to control access. AWS SSO should also have better integration with AWS IAM.
Everyone is a user, and most are employees. So that doesn't really answer my question. Users need to be stored somewhere. The question is, is AD a good place to store them. AD is a standard, is flexible, and has been around a long time. So perhaps I should ask the question "Now that we have AWS SSO, why would I use Cognito?"