Fanfic Worth a look, especially if you like Gender Flip
Gender Flip stories, by and large, don't interest me, mainly because I tend to dislike the cause(s) for the flipping. For this reason, I avoided AiTDW for a while, but once I started it, I found it to be a lot better than I was expecting. The forced cooperation between the Russian military and NERV is handled skillfully, as are Azazel's agents' interactions with the Children. The Angels are proving to be better foes than the start of the story would lead you to believe, and their reasons for what they're doing are being explored in more and more detail as the story progresses. The most interesting aspect, by far, is the change to Shinji and Misato that forms the foundation of the story. While Misako is fairly close to canon, Shinju is such a departure from canon!Shinji that she's almost not the same character, and one of the key points that keeps me reading is to see how much of Shinji still exists in her, and whether or not she will change as the story progresses. And then there's the changes to Asuka...
Now, for the downsides. Some of the more openly militaristic and propaganda-ish parts have me going cross-eyed...they make sense in-story but can be a chore to read. The Angels' characterizations may grind your gears. Asuka's father, despite being a key character, doesn't feel right for this story, and tends to stick out like a sore thumb for me. The most potentially damaging thing about the fic is that it hinges on whether or not you can accept Shinju as a character instead of Shinji; if you can't, you will probably hate it.
Overall, I would definitely recommend AiTDW if you're looking for a novel take on NGE.
Fanfic Crazael's review
The two most interesting things about this fic are what happened to Shinji and Misato, and the Azazel program. Other than those, the one thing that saves this fic in my eyes is the writing, which is superb (except for the random 2nd person scene, which makes no sense).
Fanfic unsigned review
Nine chapters are available now, which are each nearly 20,000 words long. Clever politics, clever combat tactics (possibly the most original Ramiel battle I've ever seen) and a very interesting twist on Shinji's life.
Fanfic Too much Gun Porn
A good idea ruined by the need to go overboard in militarism and darkness. All I could think of after the last chapter were the Eight Deadly Words. The moral ambiguity has devolved into outright nastiness, and really I'm now hoping the bad guys win. When you no longer care for your heroes, it is time to throw in the towel. Plus all those damn pointless crossovers and forced Shout Outs were just getting irritating.