A system and method for intelligently configuring a machine learning-based dialogue system includes a conversational deficiency assessment of a target dialog system, wherein implementing the conversational deficiency assessment includes: (i) identifying distinct corpora of mishandled utterances based on an assessment of the distinct corpora of dialogue data; (ii) identifying candidate corpus of mishandled utterances from the distinct corpora of mishandled utterances as suitable candidates for building new dialogue competencies for the target dialogue system if candidate metrics of the candidate corpus of mishandled utterances satisfy a candidate threshold; building the new dialogue competencies for the target dialogue system for each of the candidate corpus of mishandled utterances having candidate metrics that satisfy the candidate threshold; and configuring a dialogue system control structure for the target dialogue system based on the new dialogue competencies, wherein the dialogue system control structure governs an operation of an automated dialogue agent.