General changes I'd make are to get rid of the Shinji-centric nature of Rebuild, and give other characters more screen time for development. Also, no more Rei is the love interest, cause, the brother/sister angle is not my thing, and IMHO a little weird.
Rebuild of Evangelion: Legacy - 1.01 SPOILER: Show
Misato no longer knows about Lilith. That really ruins her credibility with me because she shouldn't know that, what else does she know. Does she know about instrumentality? I bet she does in Rebuild, and she hates Shinji because she hates herself for being a part of it. So her speech to get Shinji to attack Ramiel is more along the lines of protecting everyone he cares for, and protecting those that care for him, and then she lists off names, and Shinji agrees, however begrudgingly. Also added scenes of Asuka getting ready to head for Japan, and her own battle against Gaghiel, and Kaji meeting up with his ward, Mari. Also a bit more screen time for Hikari and the stooges.
Rebuild of Evangelion: Legacy - 2.02 SPOILER: Show
Opening where Mari kills Angel stays the same, as is her meeting with Shinji (cause how is that not funny as hell). Asuka's arrival stays the same, but the air force pilot at 14 is beyond implausible to me, like the world is not that desperate for pilots, adults still exist, and fighter planes are not for children, EVAs are however, so no more captain. So Asuka Langley Soryu (back to the way things should be) meets up Shinji and Rei, and they begin to become friends. Rei likes Shinji, but not in a romantic fashion, and Asuka takes the opportunity to get to know Shinji better by living with him. Also, adding back in Israfel and the ballet kill, because that should never have been left out. Ok, also no more "Three EVAs active in a country rule" cause it's bullshit. Toji is back in Unit-03 and is injured severely (but not killed) as is Rei during the fight, Shinji is fired for wrecking the pyramid (he actually is able to destroy a good portion of it before he is knocked out), leaving only Asuka to fight Zeruel. Asuka is saddened by Shinji's departure,and is almost killed in the fight with Zeruel until Mari intervenes in Unit-00, which she beasts out in. Asuka gets out of her disabled EVA, only to be grabbed by Zeruel and ingested, which Shinji sees as Mari is being defeated, and Unit-00 is utterly destroyed. He rushes to his EVA and everything else goes as planned, with him shouting "Give me back my Asuka!" and getting her back in the same fashion he rescued Rei. Also a bit more screentime for Hikari and the stooges, and Hikari and Asuka become friends, and more Shinji x Asuka time.
Rebuild of Evangelion: Legacy - 3.03-2.02 SPOILER: Show
Sets up the time in between the two stories and explains the things that happened. Mari and Rei get together (Because she looks like Yui, read the manga folks) Mari's past is explained, WILLEs formation is explained. And Kaji is in charge of WILLE, and Misato is his subordinate, and they are back together after Shinji nearly wrecks the world. It shows Mari in Unit-08, and the restoration of Unit-02 (and its S2 Engine) and its storage until they can recover Asuka and Unit-01. The story also shows a recovered S2 Engine for the Wunder being installed, and the reason to recover Shinji and Asuka is to have more pilots on their side. Also, Toji is seen alive and well, living with Hikari, and working with Kaji as his bodyguard and Hikari as his assistant. He misses Shinji and is able to convince Kaji to recover his friend from orbit to fight. The final scene shows us Unit-01 in its space crucifix and goes inside the Entry Plug to see Shinji and Asuka in a warm embrace, being kept alive and well by the S2 Engine and Yui's love for her son and his OTL. Also I have to mention, everyone ages normally, so when Shinji and Asuka wake up, they will be in adult bodies without knowing why.
Rebuild of Evangelion: Legacy - 3.03 SPOILER: Show
Ok, opens with Mari and Rei entering orbit to recover Unit-01, with Rei leading (in Unit-07 which physically looks like Unit-08 in Unit-00 second color scheme), and Mari acting as backup. Everything that follows happened in the film, excluding the mission over life philosophy (Kaji's love has kept her from becoming a raging bitch) Shinji and Asuka are recovered from the entry plug in an adult state (much to everyone's surprise) and are greeted in the medical bay by Sakura, Rei, and Mari. Shinji and Asuka freak out over their aging, and the fact that Mari and Rei are together, that and who the hell is Mari? The past 8 years is explained to them, and Rei's origins as Shinji's kinda sister, Shinji agrees to fight if Asuka does and Asuka agrees to fight on one condition, that her and Shinji share a room together. after a few days, NERV attacks with Unit-06 and Unit-09 and kidnaps Shinji while Mari tries to stop them. Rei consoles Asuka with a kiss, and Mari doesn't mind as she knows Rei had a crush on Asuka all those years ago. Shinji is brought before his father and fitted with a bomb collar to make him follow orders (unlike before). Kaworu looks after Shinji, and makes him feel comfortable by loving him, which Shinji is glad for as he feels very uncomfortable being back at NERV. Shinji is placed in Unit-13 with Kaworu, and Kaworu takes the bomb collar off and puts it on, saying that Shinji should follow his conscious, and not his orders. With a Kaworu dummy plug set into Unit-06 and Rei Q (who looks 16-ish) in Unit-09. The descent into terminal dogma goes like in the movie, with Unit-02, Unit-07, and Unit-08 intervening to save Shinji. Unit-07 fights Unit-09, and Rei kills Rei Q because "there can only be one Rei Ayanami, and that's me, father." Unit-08 fights against the accidentally awakened angel (Rei's fight knocked the spears out of place), and Unit-02 engages Unit-13 to try and save Shinji. When Shinji refuses to pilot, as the unit begins to awaken, Kaworu is killed, and Shinji is devastated losing someone that genuinely loved him, while Asuka pulls his plug out, and gets him inside her own EVA. Unit-07 is damaged and recovered by Wunder, while Unit-08 and Unit-02 fight and defeat the angel before it damages the Wunder, and are forced to walk in the wasteland to be recovered as the Wunder flies away.
Rebuild of Evangelion: Legacy - 4.04 SPOILER: Show
Rei is recovering in the medical bay after the fight and asks where Mari is. Recovery teams are sent out into the wasteland to try and find them, while Yui wakes up to go and retrieve her son. The trio in the wasteland are confronted by over 50 nemesis series, and with Unit-08 being low on power, Asuka is forced to fight on her own, until Unit-01 charges in. Shinji transfers to Unit-01 to help defeat the enemy units just as the teams from the Wunder arrive. With everyone recovered, the Wunder heads to WILLEs HQ on Midway Island. There they meet with Kaji, Toji and Hikari (Toji and Hikari are overjoyed that their friends are alive), and they discuss a final assault on NERV. Kaji shows them a picture of a creepy white Evangelion and says that 22 of them have been made, and are ready for deployment. He wants them intercepted by the Wunder and the four EVAs they have at the remains of Tokyo-3 before they can be deployed to destroy humanity. Kaji orders all four EVAs be refit, and Rei and Mari's units be installed with new S2 Engines he had recovered from a NERV outpost. Now, without the need for external power, the four pilots ready themselves for the final battle. As they arrive, Shinji realizes he must confront his father, and Asuka agrees, when the enemy is nearly defeated he should break of and find him. Armed with a shit load of weapony, and with the Wunder flying as air support, the remains of the nemesis series and the MP EVAs attack the four. The battle looks like Asuka's EoE moment on steroids, and with only 5 MP EVA's left after a knockdown drag out fight, the Wunder has taken a lot of damage and has to set down in the ocean east of Tokyo-3, and Asuka tells Shinji to find his father, and teach him a lesson. the girls finish off the rest of the MP EVAs, while Shinji confronts his father, and before he can rush Gendo, Yui takes over for a moment and devours him whole. Everyone then meets back up to destroy the fusion generators powering NERV HQ, they set their A.T. Fields at maximum and survive the blast, which can be seen from the Wunder. after the Wunder is repaired, it returns to Tokyo-3's crater and sees the EVAs have been shut down, and are patiently waiting to be recovered. With the EVAs recovered, they head back to Midway and are congratulated at a job well done. As the credits begin to roll as the pilots ready themselves for their new, Kaji tells them that as the remnants of NERV pop back up, they will be called back into action, but for now it's time to relax. Also as to why Midway isn't submerged. When 4th Impact happened, the White Moon, which was still in Antarctica, was destroyed, and it filled in with water, lowering the water levels of the planet to pre 2I levels.
Rebuild of Evangelion: Legacy - Final SPOILER: Show
4 years after 4.04 ends, everyone has become happy and adjusted to not having to fight, Shinji and Asuka have twins (a son and a daughter), and Mari and Rei have a son (from Shinji's donated sperm, he is related to Rei after all, and Mari carried it). The Earth is returning to its state before 2I, and people are thriving once again. However, the NERV bases in Germany, Russia, China, the US and the UK have just completed their nemesis series drones, which are launched toward WILLE HQ with 5 new EVAs of incredible strength, powered by a Kaworu/Rei dummy plug. The attack comes on the fourth anniversary of NERV's defeat, and everyone is scrambled to stop them before the protectors of the world are wiped out. A battle ensues where everything is nearly destroyed, until the four pilots we know and love awaken their EVAs godlike powers to utterly destroy the enemy. However one of the modified EVAs gets aboard the Wunder and takes it over, forcing Misato and the crew to abandon ship, and the pilots to attack it in God Mode. The Wunder is destroyed, leaving WILLE without its flagship, and realizing the threat of NERV is still there, the four pilots (in an awesome montage) go and destroy everything NERV has left behind before self destructing their EVAs and moving on from that dark chapter in their life.
So, there you have it DarkBluePhoenix's Evangelion Rebuild. Please leave comments on your thoughts about this story. I do intend to write it, as this is simply a very rough draft, I'll take any constructive criticism or praise you have.