MCP is essentially just JSON RPC with a few special fields that must be included. I have reservations about JSON RPC, but there needs to be some 'service discovery' layer for LLMs to interface with.
It needs to be available in places like websites, desktop applications, backend services, etc. The CLI is only one place that these systems interface with.
Whatever you replace MCP with will be in a similar shape even if you specify a different communication protocol or different fields for tool discovery.