CLI, API, MCP are all useful ways to connect. It just depends on the use case you're going for. I've used all 3 and find that they all have benefits.

MCPs are great when you just want that native out of the box low mistake way for agents to call your services it's great for certain cases.

I also developed a new method of using MCP called ADP (Agent Delegation Protocol) that sits on top of MCP where there is only 1 tool for the MCP, and when the agent wants to do something it just issues natural language commands and the ADP engine handles the rest it does all the routing etc... to the right sub-agents and executes tasks and return the results. (more on this soon).

Internally if you have a good orchestration system you do not need MCPs and can use APIs but those APIs should be designed for agents, IE based on DSLs, that project into internal operations. I do this too.

CLIs are great for testing things out, but agents often get things wrong, it's great for experimenting to see what works out of the box and what doesn't.

For me the perfect medium is a mix of MCPs and APIs. APIs are cheap if designed well, and if your workflow is a DAG then APIs are especially good because you already have a deterministic flow which means you can use small LLMs or even just something like Jev.

So my summary is:

CLI - Great for out of the box, things that are well known, where you want to verify the output

API - Great for low-cost large volume, highly repeatable workflows, that require high reliability you want your agent to execute without you having to hand hold.

MCP - Great for building debugging systems, or as an entry point to more complex workflows that you need your agent to have some ability to orchestrate.

I'm using MCP with ADP to route to large workflows that execute APIs internally for what i'm working on. So it's a mixture.