Actually, the problem users have is with the message generated by El Capitan. El Capitan's job is to screen out and correct incompatibilities it has with Java 6 or any other Java version, thereby taking that burden away from the El Capitan user.
Additionally, any software allowed to run in an El Capitan environment is known to El Capitan, so why would not El Capitan provide the user with the precise runtime identity of any such software which is telling a user to take action, without also issuing Apple's recommended solution? And no solution should EVER contain the option to install "deprecated" software into the user's experience.
A message telling me to essentially "go read something" is not the solution users paid for. Microsoft did exactly that sort of thing for years until Apple came along with a vastly superior user interface, which intelligently and correctly presented users with operating systems free of user participation in error resolution. And we certainly DID NOT pay for Apple software which suggests we install "deprecated software" to make messages generated by that Apple software disappear.
But maybe I'm just another dumb user working for over 30 years as a software development project manager for a major software solutions company in an IT world dedicated to providing users with reliable, intuitive and safe operating systems.
That's probably it...