I think you would enjoy reading
Pagan Christianity by Frank Viola and George Barna. That is if you haven't already, since you seem to be noting a lot of the same things they get into. Basically Christianity as we know it can trace much of its modern form to influences of Paganism, Judaism, and just plain arrogant people that thought they knew better than God how to run His church.
Good for you for asking the questions. Protestants of course look back at Martin Luther as a great man who challenged the unbiblical traditions of his day, but they generally fail to do the same thing themselves. And quite honestly, I think Martin Luther was rather blind to the traditions that gave him position in the first place.