A really enjoyable game. I'd like to take a moment to give my perspective as someone who has never actually played CLANNAD or seen the anime. The most I did was look at the article for the game and the characters partway through playing this game. So I wanted to chime in and say that, yes, I can confirm what some others already guessed at, this was a great game even if you know nothing about CLANNAD or the world that it's set in. The rest of my comments might possibly be a little more spoilerific, so I'll put them under tags. Just keep in mind as you read them that they are coming from someone who doesn't know the series and for all I know, some of these things could have been intentional in order to give the game a similar feel to that of the original.
Once I got into the game, I enjoyed it, but I found myself rolling my eyes a little bit at a few points during the first part of the game. Naoyuki was just so depressed and negative and introspective that it was a little ridiculous and I kind of wanted to punch him. And this is coming from someone who tends to be cynical, is extremely introspective, over thinks everything, and has a history of depression. Again, I don't know if this was just trying to match the tone of CLANNAD, but at times it seemed as though you were trying a bit too hard to give him this sort of tone and it almost came off farcical.
The other point at which I really didn't like Naoyuki was in his interactions with Shige. Yeah, Shige was kind of being a jerk, but even before he started being a jerk, it seemed like Naoyuki was going out of his way to be an ass. I mean, up until that point, all Shige had done was asked if he could talk to him and Naoyuki had even said he seemed nice, even if he afterword said that looks could be deceiving. It kind of seemed a little out-of-character for what you'd shown Naoyuki to be up until that point. He always seems to do his best to be ignored and whenever he has problems with authority figures, he deals with it through avoidance rather than confrontation (like how he didn't want to eat breakfast with his mom, even when he his teacher yells at him he doesn't really fight back, etc.) I mean, overall it seemed his problems (at least the outward ones) were of apathy rather than a bad attitude, so when he acts like that to Shige it just makes him seem kind of douchey and I almost feel like it takes away from the courage he expressed when standing up to those upperclassmen because if he could stand up to Shige like that, standing up to the upperclassmen doesn't seem like it would be so hard either. I may be rambling a bit, but hopefully you get where I'm going with this. That scene just bothers me because it seems totally OOC because it seems like it'd take a lot more to "break" Naoyuki enough that he would act, especially since he never fought back when other people were saying things about him until after he got together with Atsuko and only acted to defend others. The only other way I can see of interpreting it is that he's being a bully himself, which doesn't really say something very good about him if he's a jerk to the first person he meets who he feels is less powerful than him who says even the slightest little negative thing to him. Believe me, I've been on both sides of bullying and like Naoyuki I was bullying because I myself was being bullied, but I feel like if you want to show something like this you should do it a little earlier in the story as his life is starting to turn around thanks to knowing Atsuko (or Haruka, I suppose) at this point and that's supposed to be changing him for the better, which really made me feel like this moment came out of no where.
Augh, sorry, I talk forever. Anyway, I'd also like to agree with what someone else said about the comparative lengths of Atsuko and Haruka's paths. While Haruka's path seemed to be other before it even started, I too experienced ending fatigue with Atsuko's. I felt that you could have easily ended the game shortly after the birth of Tomoya. After all, those who are already CLANNAD fans know what's going to happen and for those who aren't, the ending almost seems to be too much. I mean, not only does Atsuko die just as the two of them are finally really happy, but Naoyuki takes to smoking and drinking (becoming everything that Atsuko's dad and his own dad were, minus the child molesting.) Yes, it does eventually get better, but I think that almost makes it worse if you don't know CLANNAD at all and then you later find out about it and find out that the "better" doesn't really last. I don't know, it's just my opinion on the matter, but I think it would have been nice if the ending wasn't quite so oppressive after we had finally gotten the game to the point where it didn't feel that way anymore.
Anyway, my only other two comments were about the cursor, which seemed kind of non sequitur and didn't seem to fit with the tone or content of the story (I can only assume this is some sort of CLANNAD reference that I don't understand) and the fact that you couldn't click to advance past the screens that said "Ushinawa 1985" and "The Illusionary World", which got a little annoying since they both came up so often.
One geeky English major comment: "The Yellow Wallpaper" is more of a short story than a novel, both in its length and method of publication. (A novel or a novella is either published all at once with its own binding and separate from any other pieces, or as was common in Gilman's day, in serialization, or short chunks of prose that would be released one at a time until it was completed. A serialized piece was released either in a magazine, which would also be serializing other works, or on its own through a subscription. It's not very common for prose to be released like this anymore, but it's very similar to how manga is released in Japan in magazines like Nakayoshi, Ribon, or Weekly Shounen Jump. Usually, once it was finished people would get all of the separate serials bound together into a complete book, often for a reduced rate as compared to what you might pay if you bought the whole book after serialization was finished. Contrast this to "The Yellow Wallpaper", which was published all at once with other short stories in a literary magazine. It was also only 15 pages or around 6,000 words, which is not nearly high enough for a novella, which has at least 10,000 words, by even the most conservative definitions, much less a novel. In fact, it's not even long enough to be considered a novelette, which is longer than a short story and shorter than a novella which needs to be between 7,500 and 17,499 words. In other words, it may be on the longish side for a short story, but it's definitely a short story and really can't be called anything else.) So, while I really enjoyed Atsuko's reference to it and couldn't help smiling a little (as I've read it for a total of three different classes), it did throw me off a little when Atsuko said it was a novel. Sorry for how geeky and nitpicky this complaint is, but it bothered me.
Hopefully those comments don't seem too negative because I really did like the game, it seemed extremely professional and it was extraordinarily touching. It's really amazing that you made this whole thing by yourself in only a year. I feel like I should be asking if you're related to Makoto Shinkai
or something. (And if you are, can you get me his autograph? XD)