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Evaluating retrieval-augmented generation (RAG) systems remains challenging, particularly for open-ended questions that lack definitive answers and require coverage of multiple sub-topics. In this paper, we introduce a novel evaluation framework based on sub-question coverage, which measures how well a RAG system addresses different facets of a question. We propose decomposing questions into sub-questions and classifying them into three types—core, background, and follow-up—to reflect their roles and importance. Using this categorization, we introduce a fine-grained evaluation protocol that provides insights into the retrieval and generation characteristics of RAG systems, including three commercial generative answer engines: You.com, Perplexity AI, and Bing Chat. Interestingly, we find that while all answer engines cover core sub-questions more often than background or follow-up ones, they still miss around 50% of core sub-questions, revealing clear opportunities for improvement. Further, sub-question coverage metrics prove effective for ranking responses, achieving 82% accuracy compared to human preference annotations. Lastly, we also demonstrate that leveraging core sub-questions enhances both retrieval and answer generation in a RAG system, resulting in a 74% win rate over the baseline that lacks sub-questions.