I haven't been able to make a coherent argument against MCP, so I've settled for "I just don't like it".

CLI tools have an edge in that their definition live in model weights; MCP requires a portion of the context for tool definitions.

Having an extra server just to orchestrate the tools, I don't like it.

For anything that does not have a native CLI tool -- just write a wrapper, a shell script, whatever performs the task adequately. It folds into the workflow nicely. Leveraging decades of unix tooling philosophy has its benefits.

Having a shell runner is just... simpler. And as another comment mentions, you can create users for the various agents to restrict their access to things, almost as if that's what users were meant for!