I don't know about anyone else, but my major disagreements with Christianity are fairly universal, foremost being a total lack of evidence to back up anything they claim.
The regular way around that is the faith gambit; something about the religion requires belief instead of knowledge.
I haven't a clue why though. Faith is something that helped killed my faith, heh.
Re: Christianity's muddled nature. The religion's been revised so many times over the years it's ridiculous. If one believes that it started out as a true religion, it's hard to argue any of the sects today resemble that original truth. That's why a bunch of the denominations claim they go back to the basics, or fix the problems introduced over time, etc etc. This is a big part of Mormonism, for example, as Joseph Smith rewrote small portions of the bible to remove ambiguity and of course introduced his supplement in order to remove even more ambiguity*. But of course, these denominations also change over time, kinda removing any legitimacy to their claim of objective truth.
So to any Christians, I really suggest you make your own interpretation instead of following any specific denomination's. They really have no better claim to being "right" than you, so pick what feels right to you.
*As a former Mormon, I will note that the changes to the Bible, though small, didn't really remove any ambiguity at all, and honestly seemed quite random. None of the changes were all that big, and you can still find conflicts with other portions. The BoM though was extremely blatant with little room for different interpretations, so that's a plus I guess?