These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Awesome Music: The soundtrack. Yes, there is a soundtrack to a doujinshi manga. However, special mention goes to "Girl" and "Holy Day". These can be heard either here for just the soundtrack, or here for select scenes included (all ages friendly, no adult content included). One is a playlist, the other is 4 part youtube clips.
Ending Fatigue: One of the "strikes" against the series. There are a few moments of, "Aw, that's a good ending... oh, wait, there's more."
Fanon Discontinuity: Fans of the work usually like to pretend that 1.5 doesn't exist since it's out-of-character smut. Skipping it won't affect the flow of the main story at all, except for the reveal of Asuka's pregnancy which is arguably handled much more gracefully in 2.
Fight Scene Failure: One of not when Rei is using the positron rifle against the MP Evas. In one panel the shot she fires is clearly about to hit an Eva in the head, but the next panel has the shot hitting it in the stomach.
Iron Woobie: While Shinji was debatably this in the original series, he certainly fills out this role in this story. This is best exemplified when he goes off to fight the MP-Evas to save Tokyo-3, even though he knows it's essentially a suicide mission.
Jerkass Woobie: Ghost-Asuka is far more cruel and mean-spirited than she ever was in the main series, but that's hardly surprising considering what she went through.
Moral Event Horizon: SEELE's actions during the series take on the events of end, where like in the normal series, the virtually destroy Tokyo-3 and fully intend to murder everyone in NERV. Thankfully they don't get away with it this time.