A lot of people have asked me why Fuko's story is the first arc. They're off-put by the oddness of her story, by her, by... well... it's Fuko! These same people ask why Kotomi wasn't shown first, since she's a bit easier on the brain, not to mention reality. What these people don't seem to get, however, is that Clannad is not a serialized TV production, but a serialized adaptation of a visual novel. These are chapters in one long story, not a bunch of smaller stories that are interconnected. Like any good novel, Clannad's chapters build up the body of a thesis the author has about reality. The beginning chapters lay out the problem and the basic blueprint for solving the problem. The later chapters put this blueprint into action, albeit in a way that's different than the blueprint.
Fuko's storyline is that blueprint.
Consider the problem: Tomoya is unhappy and his family is broken. Solution? Get a bunch of friends and make a new family. Something that won't fall apart. Tomoya already chose Nagisa, even if he isn't completely aware of his choice yet. The issue that comes up is that Tomoya believes he can do it alone, that he's able to carry on without the help of others. While he helps others, Tomoya doesn't really accept all that much help, and even then it's after an argument. This gets exacerbated even worse in After Story, where Tomoya receives the help of his new in-laws with no grace whatsoever. Tomoya believes he is an island, an entity unto himself...
|OK, he's wrong here.|
|And here too. Funny, that...|
Fuko's the first arc because she initially shows Tomoya how to save Ushio: by calling on the people of the world, on reality, on God to solve the problem. Tomoya and Nagisa's parts are to help Fuko realize that she can and should ask, to have faith in, well, everything. She shouldn't shoulder the burden by herself, and neither should Tomoya! The thing that distinguishes Fuko's arc from Kotomi is a sense of almost irrationality about Fuko that we never witness in Kotomi. Kotomi believes she can solve the problem, hell, she doesn't think there is a problem with what she's doing. Fuko, however, knows what she wants, she just needs to know to ask for it. Her cry is desperate and strong, and mirror's Tomoya's own cry at the end of After Story in a way that's almost too much of a match to not notice after watching it for the 50,000th time! Also of interest is the fact that both these characters are in somewhat similar situations. Tomoya is paralyzed by his depression and his hurt, and Fuko was banged up that she's in a coma. But even there, at these characters' low points, they find people willing and able to help them. Fuko gets Tomoya and Nagisa when she needs help. Tomoya gets Ushio and Akio.
To keep cementing the point Fuko shows up at certain points of Tomoya's life where he's wondering what he's going to do. She keeps pushing him towards asking for help, for getting aid, for not striking out on his own, even at the cost of hilarity. She keeps trying to show Tomoya what he unintentionally showed her: you must ask for help, because only with others can your goal be reached. Fuko is at the beginning, because you need to know what's going to happen at the end: a miracle.