1.11 You Are (Not) Alone pretty much is a recap of episodes 1-5 with some minor alterations, namely Shinji being less of a bitch, but still emo. It has a pretty d'aww ending too with an appearance by Kowaru.
2.22 You Can(not) Advance is where the story makes its first and big deviation from the series namely with the introduction of Mari, the British eva pilot
[video=youtube;2FCbhCD4M_U]http://www.youtube.com/watch?v=2FCbhCD4M_U/video]
Shinji's friend is no longer a pilot. I won't give other changes because they are plot related.
3.33 Q Quickening is the third installment and is the beginning of the end of the story. This one is completely original and separate from 1 and 2 which were still retelling most of the original series. 4 will be the end over all.