Catholicism is a compromise reached between Christianity and paganism, otherwise they would have never won people over to Christianity. Today it serves it's own existence so it can make innumerable concessions to science as long as it does not threaten it's existence. And if kept out of politics, it will gradually revert to it's original function: a simple teaching institution. You can observe that the Church did revert to that at one point, with establishment of libraries and universities, after it had sated itself in the blood of countless victims. And that was when it's dissolution was at hand.
Protestantism is pure, unadulterated, rejuvenated, and revitalized Christianity, in full contact with it's idol destroying roots. Moralism is poisoning and Protestant ministers have been the Pharisees of our times. They serve an arbitrary god, made even more arbitrary by the freedom of interpretation. They derive great advantage from being split into thousands of sects, they are a diaspora akin to Judaism. A multi-headed hydra has been unleashed upon the world.
Both have their ups and downs, but I've always been more inclined to side with the Catholics. I admit that Luther had good intentions and paved the way for manifold reformers, thinkers, and artists, but he made a tremendous mistake in reviving fanaticism, the Catholic Church reacted vigorously to his reforms and this led to the 30 year war.