The flaws I have spotted over time have more to do with how Sikhism is practiced and understood by some individuals. I have not identified flaws within Nanakian philosophy. There are areas of theology that I don't think have been well explained, and the same goes for areas of contradictory meaning for some ideas like reincarnation. But again, the flaw is not within Nanakian philosophy but rather with how Nanakian philosophy is interpreted.
Let me give you a more personal example. For a long time I struggled to understand why anger is a basic evil. My search on this forum and in other readings written by Sikh scholars were not helpful. Only after a systematic study of Buddhist thinking did I get the answer. When I applied the Buddhist understanding to Gurbani there was no inconsistency. Buddhist scholars in this instance were more helpful than Sikh literature on the subject. Why?
Well this is my intuition only. Buddhism has a longer and fiestier tradition of "teaching." Within Sikhi we have a very hard time with two trends, and I see this on the forum every day. First, among many Sikhs, there seems to be unwillingness to allow debate, and by that I only mean friendly intellectual debate. By contrast, in Judaism there is a centuries old tradition of religious argument among students and teachers that helps to clarify important ideas. Rabbi's and scholars debate with the intention of finding common ground and consensus on the meaning of scriptures. Among some Sikhs, intellectual arguments too often end with accusations of heresy and name-calling across the board. Second, there seems to be among some Sikhs another pattern: unwillingness to explore, probe, and analyze altogether. So rather than engage in serious elaboration on an issue, there is mad-cap posting of Gurbani with little if any explanation. Or someone will say, "There is no point in discussing this any longer. The matter is settled. We should all now be quiet." Of course, there are glorious exceptions to what I am saying, such as the kathas of Sant Muskeen Singh ji. But even with this example, I don't see serious discussion. Rather there is a kind of mum acceptance of what he has said; or wild accusations of heresy against him because he quotes Urdu poets.
So the flaws are in the application of Nanakian philosophy, not in Sikhism itself. Again forgive me if I have offended anyone. These are my opinions.