This is pretty fair: in claude code, I have the github mcp server installed, but the agent actually prefers to use the CLI. There's also other advantages too, such as incremental discovery of subcommands for more complex CLIs. Certainly agents already don't have a problem using CLIs.

That said, this doesn't fully work in environments on websites like claude.ai. Perhaps you could have an org-wide Dockerfile or something that opens every time you start a chat which gives it MCP-like capabilities, but that sounds more complicated in many ways than what MCP does. There's also more problems that MCP solves, like with Prompts and Sampling (which are pretty under-used at the moment), and there aren't great analogs for that in the CLI world.

Also developers like you and I might find it trivial to install CLIs, set up auth, and open an agent locally, but this isn't widely true. As an example, at Stainless we have non-engineer folks who ask questions like "who are the most interesting people who have signed up yesterday", and with the right MCP tools wired to claude.ai, claude actually does an excellent job of answer these kinds of questions, all in the browser. This was all without a doubt possible before MCP, but MCP reduces the friction enough, such that it becomes worth-it/easy-enough to develop these tools.