|The School of Athens, by Raphael|
The works of Plato, Aristotle, Aquinas, Newton, Descartes, Locke, Hume, and Kant are full of flaws and inconsistencies, and yet these philosophers have made highly fruitful contributions in the development of our modern world. There is no reason to believe that a self-consistent system will contain more truths than the one that is not self-consistent. In fact, most self-consistent systems in history are totally false (like the religious doctrines).
One of the most important lessons of history of philosophy is that a philosophical system without any inconsistencies is unattainable, and those who try to create such a system often end up creating a cult (religious or secular).