Running both MCP and CLI-based agents in production, my take is that this isn't an either/or question.

MCP shines for stateful integrations where auth and session management would be painful to handle in CLI scripts. Think Notion databases, Stripe dashboards, calendar APIs - things where the agent needs to maintain context across multiple operations. The tool descriptions in MCP also let you embed domain knowledge that's hard to capture in --help output.

But for anything involving file manipulation, git, build systems, or standard dev tooling? CLI wins hands down. The composability point is real - being able to pipe output through jq or redirect to a file gives you flexibility that MCP can't match. And as noted, LLMs have been trained on mountains of CLI usage patterns.

The hybrid approach that's worked best for us: MCP for external service integrations, CLI for everything else. Let the agent write and execute shell scripts when it needs to chain operations - that's when you get the best of both worlds.