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The flourishing of knowledge graph (KG) applications has driven the need for entity alignment (EA) across KGs. However, the heterogeneity of practical KGs, characterized by differing scales, structures, and limited overlapping entities, greatly surpasses that of existing EA datasets. This discrepancy highlights an oversimplified heterogeneity in current EA datasets, which obstructs the exploration of the EA application. In this paper, we study the performance of EA methods on the alignment of highly heterogeneous KGs (HHKGs). Firstly, we address the oversimplified heterogeneity settings of current datasets and propose two new HHKG datasets that closely mimic practical EA scenarios. Then, based on these datasets, we conduct extensive experiments to evaluate previous representative EA methods. Our findings reveal that, in aligning HHKGs, valuable structure information can hardly be exploited, which leads to inferior performance of existing EA methods, especially those based on GNNs. These findings shed light on the potential problems associated with the conventional application of GNN-based methods as a panacea for all EA datasets. Consequently, to elucidate what EA methodology is genuinely beneficial in practical scenarios, we undertake an in-depth analysis by implementing a simple but effective approach: Simple-HHEA. Our experiment results conclude that the key to the future EA model design in practice lies in their adaptability and efficiency to varying information quality conditions, as well as their capability to capture patterns across HHKGs. The datasets and source code are available at https://github.com/IDEA-FinAI/Simple-HHEA.