I read the original version a few years ago and read the new version when it came out, and I thought that the name changes were pretty amusing. qntm kept the story as close to the original as possible while still making it a legally distinct work for copyright purposes. It's like those off-brand Froot Loops called "Fruit Spins" that are juuust different enough to not get into trademark issues. Except in Antimemetics' case, the "knockoff" version was made by the creator of the original, which I think is pretty funny.

I've heard a lot of romance novels are fanfic with the names changed, or at least that's what people say about Twilight and 50 Shades.