There are a few problems I have with Islam.
1. The honour crap. Honour Rapes and Killing.
Killing your sister if she had sex out of wedlock. Raping women who cheat on their husbands.
2. Female circumcision and genital mutilation.
3. Apostasy
4. Jihad
5. Inequality of Women and other minority religious groups.
Women have farless rights in most of the Muslim world and in the strict states like Northern Pakistan, women are forbidden to go to school, Burka's. Need to be accompanied by a male family member.
I think most religions have very similar goals, however I think that Islam is being sideswiped by some extremely hardline and Conservative groups.
Until the moderates start dealing with these hard line elements, the gap between western thought and Conservative Islam will only grow.