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The optimization of parallel I/O has become challenging because of the increasing storage hierarchy, performance variability of shared storage systems, and the number of factors in the hardware and software stacks that impact performance. In this paper, we perform an in-depth study of the complexity involved in I/O autotuning and performance modeling, including the architecture, software stack, and noise. We propose a novel hybrid model combining analytical models for communication and storage operations and black-box models for the performance of the individual operations. The experimental results show that the hybrid approach performs significantly better and shows a higher robustness to noise than state-of-the-art machine learning approaches, at the cost of a higher modeling complexity.