The current graph neural network (GNN) systems have established a clear trend of not showing training accuracy results, and directly or indirectly relying on smaller datasets for evaluations majorly. Our in-depth analysis shows that it leads to a chain of pitfalls in the system design and evaluation process, questioning the practicality of many of the proposed system optimizations, and affecting conclusions and lessons learned. We analyze many single-GPU systems and show the fundamental impact of these pitfalls. We further develop hypotheses, recommendations, and evaluation methodologies, and provide future directions. Finally, a new reference system is developed to establish a new line of optimizations rooted in solving the system-design pitfalls efficiently and practically. The proposed design can productively be integrated into prior works, thereby truly advancing the state-of-the-art.