In general the advantage of MCP would be the possibility for a fine grained control over the tools the agent is allowed to use. But unfortunately there is a myriad of nightmarish awful mcp servers around which are worse than direct API access or even a cli integration.

I wont advertise any commercial mcp I use but to give an example for a well designed and useful mcp server I could name the nixos mcp. Its useful because it bundles all the nix resources to one endpoint which is more efficient than web search and gives you better control over the sources.

https://github.com/utensils/mcp-nixos

Another one would be this filesystem mcp which is in my opinion to prefer over direct cli access. Of course this depends also on your general sandbox strategy but if you just use a generic docker image there are still many potentially dangerous binaries available and such an mcp can restrict the models capabilities.

https://github.com/modelcontextprotocol/servers/tree/main/sr...

And of course there are many service provider offering their mcp with its own llm / agent behind e.g. most web search provider. In this case you most likely already use an mcp without noticing it.