This is actually one of my favourite yaoi stories. It's very dark, but I think its darkness is sincere and thought-provoking. It is the only example of its genre to have legitimate philosophical content that I can think of. It is worth more than the sum of its parts as a result.
Yuri 'decides' that Nagi is who he says he is in spite of evidence to the contrary; but Sakura thinks that their individual experiences tie them more meaningfully than any objective event and their happiness, whatever method is used to achieve it, should be their great aim in life. This is a rather individualist/existentialist/nihilist/whatever message. You likely won't find it palatable, but it's not meant to be an easy read.
Story aside, the artwork is classic early Ashika Sakura; slightly stiff and samey but pretty characters in timeless plain clothing, slightly awkward backgrounds and cityscapes, general minimalism and high-contrast monochrome. It has a strong Tokyo Babylon influence and vibe to it, which is plausible as it was created in the early 90s. I like that kind of style, but I admit that it's not CLAMP-brilliant in execution here, only good enough to be enjoyable.
One major annoyance I have is with Zetsuai. It might seem rude to say this as they're the only group to have even worked on this manga, but frankly, they did a mediocre job in (partially) scanlating this work. Compare their version of Yuri's opening monologue with this reviewer's:
http://www.senshigakuen.com/aqua/manga/series/sekai.html
A real shame, because this deserves better. I'm considering buying it, learning Japanese and uploading it myself, just for this one. As a last resort I could just rewrite it to make it more elegant.
As a side note, I just thought this story would make a good (though controversial) short film. A TV or made-for DVD one, starring some beautiful Asian boys. It wouldn't be too difficult or costly to adapt it well and it would be a unique piece of artsy yet fangirlish entertainment.