Can Deep Research Agents Retrieve and Organize? Evaluating the Synthesis Gap with Expert Taxonomies

Deep Research Agents increasingly automate survey generation, yet whether they match human experts at retrieving essential papers and organizing them into expert-like taxonomies remains unclear. Existing benchmarks emphasize writing quality or citation correctness, while standard clustering metrics ignore hierarchical structure. We introduce TaxoBench, a benchmark of 72 highly-cited LLM surveys with expert-authored taxonomy trees and 3,815 papers mapped to paper categories. TaxoBench evaluates (1) retrieval via Recall/Precision/F1, and (2) organization at a leaf level (paper-to-category assignment) and a hierarchy level via novel metrics, namely Unordered Semantic Tree Edit Distance US-TED/US-NTED and Semantic Path Similarity Sem-Path. Two modes are supported: Deep Research (topic-only, end-to-end) and Bottom-Up (expert paper set provided, organization-only). To distinguish disagreement with a single expert reference from genuine model failure, we explicitly partition findings into capability-based (reference-free) and alignment-based (reference-dependent). Evaluating 7 Deep Research Agents and 12 frontier LLMs reveals a dual bottleneck: capability-side, the best agent retrieves only 20.92% of expert-cited papers, and 1,000 model taxonomies show 75.9% sibling overlap, 51.2% MECE violations, and 83.4% structural imbalance, all detectable without any reference; alignment-side, all 12 LLMs converge to Sem-Path 28--29%, well below 47--58% achieved by three independent human-annotator groups on the same paper sets. Our benchmark is publicly available at https://github.com/KongLongGeFDU/TaxoBench