MCP needs to be supported during the training and trained into the LLM whereas using CLI is very common in the training set already. Since MCP does not really provide any significant benefits I think good CLI tools and its use by LLMs should be the way forward.

This is very developer centric. While Github might have good CLI, there's absolutely no point in having most services develop CLIs and have their non-technical users install those. Not only is it bad UX, but it's bad from security perspective as well. This is like arguing that Github shouldn't have GraphQL/Rest api since everyone should use the CLI.