CLI is great when you know what command to run. MCP is great when the agent decides what to run - it discovers tools without you scripting the interaction.

The real problem isn't MCP vs CLI, it's that MCP originally loaded every tool definition into context upfront. A typical multi-server setup (GitHub, Slack, Sentry, Grafana, Splunk) consumes ~55K tokens in definitions before Claude does any work. Tool selection accuracy also degrades past 30-50 tools.

Anthropic's Tool Search fixes this with per-tool lazy loading - tools are defined with defer_loading: true, Claude only sees a search index, and full schemas load on demand for the 3-5 tools actually needed. 85% token reduction. The original "everything upfront" design was wrong, but the protocol is catching up.