The plot is complicated, and there are more and more questions that pile up as the series goes on, but the journey toward those answers is fascinating, fun, and deeply layered in mystery. I can't help but read on because I want to know more. I want to find out what's really going on.
It seems pretty straight forward at first--guy gets stuck in a very real sort of virtual reality and has to deal with all kinds of Edo world people and demons (and that's as far as the plot goes in the anime), but it's sooo much more interesting than that. The plot has two main sides: the things that happen to Tokidoki in the Edo fantasy world, and the mystery and intentions behind the high tech company that seems to have created this world in the first place. The possible connections between the two are dangled tantalizingly just out of reach. You get bits and pieces of the puzzle at a time, and as a reader you have to try to put them together while the characters face the dangers of a world constantly on the brink of two different wars: that tension between humans and demons and between the Japanese traditionalists and foreign "barbarians".
I think the main reason so many are confused is because of the amount of historical allusions and mythology that's packed into this story. There's also a good amount of science and psychology. Not to mention a few philosophical questions scattered throughout. This is the kind of manga that makes you think, and yet still makes you laugh and cry and feel horror. That's sometimes kind of hard to find all in one story.
The art is also amazing. I envy the author's drawing talent. Lots of detail and fine lines and the covers have a beautiful coloring style. The character's expressions (especially Tokidoki's smile) seem a little weird at first, but I now feel like there was a reason Toki's smile always seemed a little off back then. His problems went a little deeper than you'd think at first, and the character development he goes through while wading through them is subtle but feels really meaningful. At the same time, you can't really take him too seriously. He's still a goofy nut at heart, and plenty hilarious sometimes.
I just wish they would publish this in English already. I would buy this one, and I don't understand why they would sell the anime and not the manga when the manga is worlds better. Come one.