To me it depends on the intended use:

- MCP - if you need discoverability. a great example for this is something like context7

- CLI/API + Skill: When you have a defined workflow you want to use. For me a good example of this is using the Linear GraphQL API instead of their MCP

I prefer the Linear API because, where I work, we have come up with our way of using the tool so I don't need the entire MCP to do what I need the agent to do. I think for most use cases an MCP is a waste of context.