My favourite manga changes:
Toji dies instead of being hospitalised and forever offscreen
Rei doesnt slap Shinji on the escalator she's a lot more emotionless in the manga. I also like the funny scene where she fills a cup with tea leaves
A lot of Angels that felt like filler to me and a lot of the fan service is cut. In particular the volcano episode felt particularly fan servicy and I didnt really like the computer virus angel. The forever walking robot also felt like filler. Almost every episode that was cut from the manga was one I did not enjoy.

I just thought i'd post my thoughts before I go back and read your cruel angel thesis