I’m trying to use the CLI whenever possible - it’s much easier to install and can be used by both me and the agent. For example, gh seems much easier than installing and setting up an MCP server connection, and it’s more human-readable in terms of what the agent is calling and what it’s getting in return.

For other integrations, I first try to find an official or unofficial CLI tool (a wrapper around the API), and only then do I consider using MCP