One big problem is the existence of Hadith, and how entrenched it is in Muslim culture. Throughout history, any ruler who wanted to make up a "doctrinal" point would come up with a supposed ruling by Prophet Mohammad to support his claim. So we ended up with 10s of thousands of doctrines that can be used to justify whatever the hell one wants. And given the nature of those who created Hadiths, one cannot be surprised that many of them can be extremely backward and harmful. For example, the entirety of Sharia laws comes from Hadith.
And it isn't like you can safely challenge those doctrines. A couple of years ago, I mentioned the unreliability of Hadith to a relative in a discussion about religion, and we almost came to blows. It is just too deeply entrenched in the the culture.
