Graph Neural Networks (GNNs) have achieved remarkable success in various applications, but their performance can be sensitive to specific data properties of the graph datasets they operate on. Current literature on understanding the limitations of GNNs has primarily employed a $\textit{model-driven}$ approach that leverage heuristics and domain knowledge from network science or graph theory to model the GNN behaviors, which is time-consuming and highly subjective. In this work, we propose a $\textit{metadata-driven}$ approach to analyze the sensitivity of GNNs to graph data properties, motivated by the increasing availability of graph learning benchmarks. We perform a multivariate sparse regression analysis on the metadata derived from benchmarking GNN performance across diverse datasets, yielding a set of salient data properties. To validate the effectiveness of our data-driven approach, we focus on one identified data property, the degree distribution, and investigate how this property influences GNN performance through theoretical analysis and controlled experiments. Our theoretical findings reveal that datasets with more balanced degree distribution exhibit better linear separability of node representations, thus leading to better GNN performance. We also conduct controlled experiments using synthetic datasets with varying degree distributions, and the results align well with our theoretical findings. Collectively, both the theoretical analysis and controlled experiments verify that the proposed metadata-driven approach is effective in identifying critical data properties for GNNs.