Fanfic
Full disclosure, I know next to nothing about the Warhammer verse. I've never played it, and I've never read any of the background material, so I can't really appreciate how it would impact the Eva verse when the two cross over. I eventually decided to read this story because it's so well known among fanfic readers and overall impressions seemed to be positive, and I was curious.
I kind of wish I hadn't.
I will say that the writing is impressive, in two ways. First, because the author manages to create drastic, nigh ridiculous changes both within and among the characters of the story, without changing a single aspect of how the overall story arc progresses. I'm serious. Despite having nearly godlike powers, radical changes in their biological composition, even causing the Evas to develop new aspects, and with vastly improved resources and weaponry, the sum total impact of all of these changes against the original plot of Evangelion is: fuck all. This makes the story appear less like an exploration of divergence and more an experiment in wish fulfillment of the worst kind. To make it more clear, yes, the Angels are engaged in new and different ways, and victory is achieved via means not seen in the original. But Shinji still only wins by default against Sachiel. Shinji and Asuka still lose their first round to Israfel, are forced into cooperative syncronization, and win round 2. Bardiel still ends in tragedy because the Dummy Plug was turned on. Shinji still syncs above 100% and gets absorbed by Unit 01 while fighting Zeruel as the Last Man Standing. Asuka still gets mind raped by Arael. Rei still dies in a Taking You with Me against Armisael. How can so many changes in the characters mean so little in the grand scheme of things?
Second reason this story's writing impressed me: the author often uses three paragraphs to communicate something that can easily fit within three sentences. There's Purple Prose, and then there's pointless repetition. The author isn't doing this to be florid - at least, I don't get the impression that that is the goal here. No, they just want to make sure that the reader really, absolutely, definitely gets the point, by hammering it in several times in a row, every time they want to make one. We get it, Shinji is clever. We get it, Asuka is angry. We get it, the new weapons are cool. Now can we please get back to the story?
TL;DR - Neat concept, poor execution. Will not re-read.
Fanfic The End of All Your Fun
Put simply: Thousand Shinji is a Possession Sue story of the worst kind.
Now this isn't unusual on this page. There are stories that could answer to that description that I've written good reviews for. (Shinji and 40k comes to mind.) This is because they did something interesting with the premise, because they knew how to deploy the Holy Shit Quotient for sufficient awesome to keep you interested, they didn't take themselves deadly serious, they didn't depict the reality the author likes as opposed to the reality the characters he likes would create.
Thousand Shinji doesn't. The story takes itself deadly seriously, and creates the reality that the author wants rather than the one that his characters would actually make. It doesn't do anything interesting with its premise, and it gets even less interesting the more you read. But most damning, most boring, is that it can't deploy the HSQ in its favor. The victories unroll in a mechanical, foregone fashion, not just failing to create dramatic tension but failing to even look that cool while doing it.
Fanfic Comartemis' review
This troper will grant this one a tentative recommendation with the footnote that he greatly prefers S&W40K's execution.
Fanfic Earth Scorpion's review
In addition to the previous, the fact that it is a) completely awesome, and b) does a much, much better job at merging the settings, rather than just crossing them over, than Shinji and Warhammer 40k.
Fanfic GentlemensDame883's review
I'll give Thousand Shinji a thumbs-up, if only because of the final passage, which is an absolutely hilarious riffing of the "summary" that prefaces the Warhammer 40000 books. Though it of course has more merits than just that.
Fanfic Shinji becomes Light Yagami
TL;DR - A Shōnen Fix Fic variation of the original story's events, with 40k elements sprinkled around. Ignores the casts's existential issues of the source material. Recommended for fans of action-packed and teenage-oriented fics.
Despite having superficial knowledge about the 40k lore & universe, it was not difficult to follow the story. The action sequences were detailed, enjoyable and brutal, with many battles deviating a lot from the source material (like the Sandalphon, Ireul & Ramiel battles), but still strictly following the original plot milestones.
Another strong point of the story is the Chaos Gods, who represent philosophies . For example, Nurgle, who Rei ends up following, represents not only the despair of death, but also the cycle of life and encourages Rei to continue fighting. The Units' customization to represent the gods they were based into was a nice touch, too.
I had a problem with the characters, who were "edgier" in order to become more competent: Shinji was extremely manipulative to the point of almost becoming a jerk (like father, like son) and brought in mind Light from Death Note, Asuka was even more short-tempered, Rei even more obsessed with Shinji and her clone condition and Gendo was so hideous and cruel, to the point of being unrealistic. The "edgy" element was at least watered down with some humane moments, like Shinji accidentally calling Misato "mum" once and then bursting to tears, but in general it gave me the impression of a traditional action Shōnen anime feeling.
Also I heavily disliked some lewd scenes involving the general love triangle between Shinji, Rei & Asuka and the excessive fanservice of the party scene. It was like pausing the plot for adding some sexual fantasy in the story...
In general, it gave me the impression of a Fix Fic, with the protagonists not being a psychological mess, but hyper-competent to the point of killing the dramatic tension, just like the pilots from Pacific Rim: Uprising.
Some funny moments: