Matched Capabilities, Different Behaviors: A Controlled Study of MCP and CLI Interfaces for Language Agents

How much an AI coding agent costs to run can depend more on the agent scaffolding that drives it than on the interface through which it reaches its tools. We set out to measure the cost of tool use over the Model Context Protocol (MCP) against tool use over an ordinary command-line interface (CLI), a difference on which published estimates disagree by more than an order of magnitude while resting on practitioner reports that cannot be reproduced. We ran one fixed software task -- six operations against a private online git repository -- across seven agent scaffoldings and five language models, and we verified completion by inspecting the repository state rather than trusting the agent's self-report. The dominant effect was the scaffolding. Two of the seven ship no MCP support at all; they completed every run using only the CLI, which shows that MCP is unnecessary for this class of work, and they were 5.0x to 28x cheaper than the five scaffoldings that do support MCP, comparing CLI runs alone with no MCP server attached anywhere. The effect was largest for a small 27-billion-parameter model running locally, whose cost varied 139x across scaffoldings while it completed the task under all of them. The comparison we set out to make proved unstable: thirteen strictly paired MCP-to-CLI ratios span 0.43x to 29x, with outliers on both sides. The two interfaces separate on the cost of failure, where 12.9 per cent of the money spent on MCP runs bought no completed work against 2.2 per cent on CLI runs, but not on its frequency: failures were equally common in both, in the original runs and in their repetitions alike. Agents frequently ignored the interface they were assigned, so comparisons that do not verify actual behaviour measure an unknown mixture. The harness, the task, the verification and the complete dataset are released as open source.

The Model Context Protocol provides a shared interaction substrate for the agentic web, allowing heterogeneous services to expose capabilities through a standardized interface. Learning to use this ecosystem entails a hierarchy of capabilities: tool-format skills, server-level transfer, and cross-server composition. We present MCPDisCo, an ecosystem-scale reinforcement learning framework for MCP-native agents. Using a Thought-Markov Decision Process (Thought-MDP), the framework explicitly represents internal reasoning alongside routing, execution, and termination and trains on real-server, long-horizon interactions spanning 70 MCP servers and 527 tools across six domains. We study the reasoning--tool seesaw, a joint-learning failure mode in which improvement in one objective can accompany deterioration in the other. To mitigate potential interference, MCPDisCo combines token-masked reward attribution with bidirectional gradient surgery: the former separates direct supervision for reasoning and action spans, while the latter removes conflicting components from both objective gradients in shared parameters. MCPDisCo achieves higher success with fewer chain-of-thought tokens. On the out-of-distribution MCP-Atlas and the GAIA benchmark, MCPDisCo maintains monotone gains, confirming that the learned behavior generalizes beyond the training server distribution and broader agentic tasks. Model weight and implementation are available.

As LLM agents increasingly interact with external tools through standardized protocols such as MCP, tool-interface design becomes a critical yet underexplored factor. How funψtionality is decomposed into tools affects whether an agent can select the right tool and construct valid arguments. This choice is especially consequential at the edge, where resource constraints limit which models can run locally and scaling up is often not an option. We present MCP-GRANITE, an open-source extensible benchmark framework that treats tool-interface granularity as a controlled variable for MCP-based agents, evaluated under edge and IoT scenarios. It comprises 81 multi-step scenarios across 9 domains, instantiated at 4 granularity levels from fine-grained primitive tools to a single tool. We evaluate 9 locally deployed models (268M-20.9B parameters) across 8,748 trials using task completion, tool selection F1, argument accuracy, latency, and resource-usage metrics. Results show that a 4-tool interface offers the best trade-off, improving task completion by 16.4% over fine-grained primitives and 33.6% over a single monolithic tool, while nearly doubling argument accuracy. Model size is only weakly correlated with task completion and strongly with latency, while its association with argument accuracy is less robust, and a 3.2B model at the optimal granularity outperforms a 20.9B model at a mismatched one. These findings identify tool-interface granularity as a key design parameter for MCP-based agents.