Some flaws, but still very good.
I'm just reviewing the All Ages version. I haven't read the longer version, and I almost certainly never will.
I went into this expecting to read an above-average fanfic. Thus, I was pleasantly surprised when I found this to be pretty good even by "professional" standards.
The artwork is great. There was no point where I saw an image and thought "Okay, this is off-model" or such. Of course, I didn't inspect every single picture with a microscope.
I liked the concept and, for the most part, the plot. Although I may have missed something, I think there are a few plot holes here and a few contrived coincidences there. For the life of me, I can't figure out why Asuka lost her memory. Shinji, yes, but Asuka?
Otherwise, the plot is as good as one would expect from Evangelion. Between Shinji, Gendo, SEELE, Asuka, Ghost Asuka, and the ...(trying to avoid spoilers)... odd relationship between Shinji and the universe, the end result looks like something out of Light Yagami's nightmares. I love it.
There is one defect in the story which must be addressed, and I think it fits the best under "plot". The first volume of the story is simply not as good, maybe not even half as good, as the second and third volumes. The relationship between Shinji and Asuka is rushed, as is Shinji's character development and the Angel battles. I got the feeling that the author had the later volumes done in his/her head first, and that the first was just them trying to quickly get the background facts in.
My last point is characterization, which probably makes up the highest and lowest points of the story. The characterization of Asuka and spine-ified Shinji is better than any fanfic I can think of off the top of my head. Matter-of-fact, Asuka is written so well that the author had to throw in a contrived coincidence in the near last scene in order to prevent a downer/bittersweet ending. However, the author doesn't seem to have a good grasp of Rei's character. She was kinda OOC in later volumes, and jarringly OOC in the first volume.
All in all, I think this is more than worth the read, and I like to think of it as an alternative ending to End of Evangelion, despite it's flaws.
(Note, this is my first review, if anyone thinks I revealed/spoiled too much, please comment and I'll change it.)