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.