I could write a 2000 word summary about how I interpret the show to be like… but I guess I’ll make it as brief and clear as I can…

First…
Lets look at this chronologically.
1. Yukine’s explanation of existence of light orbs.
2. Kotomi’s parent’s research on different worlds.
3. Akio prayed for Nagisa.

The above proved that… City is magical to begin with. (Keep this in mind)

Second…
1. Tomoya help people out, everytime he did, a light orb appears. (As seen in more than several cases, it’s especially obvious in Yukine Arc)
2. Nagisa’s departure, but Tomoya have yet to receive a single light orb. He wished that he never met Nagisa. (No orb, no wish)(Part one of foot of the hill event… will explain below)
3. Reconcile with Ushio, bawww….
4. Reconcile with his father! Great… to add to that, he receive a light orb, it landed inside him. (Ushio noticed it, Tomoya didn’t)

Hold on…
5. Living with Ushio, living a new life, new reason to keep working hard, for the ones he loved and love.
6. Ushio’s departure, he cried. He suffered a lot, he don’t even know whether he should’ve met Nagisa. (This time, with a light orb, CRAP!)

Lastly…
7. Light orb take him back to the foot of the hill. (The part 2 of foot of the hill event)
8. He would’ve picked “Not meet Nagisa”! HOWEVER!!! By that point, he have learnt that despite the ending he “will” eventually faced, he never regretted meeting Nagisa, he called out to her, and embrace her. “I’m over here”
9. Light orb grant his true wish, to be happy.

After Story’s amazing writing is a double edge sword.
1. Amazingly written sad scene, strongly focus writing.
2. People that are too drawn to the sad scenes may lose sight of what seem to be the minor details. (Yukine’s story and Kotomi’s parent’s research)

In conclusion…
After Story, is an amazing piece of work. The sad scenes were so sad and well written that people forgotten that the town is magical to begin with. And the light orbs are not just there for show. It is only natural for people to not get the show and begin to resent it for apparently having happiness shot out of no where, when in reality, it is all made out to be…

The End

I could write a 2000 word summary about how I interpret the show to be like… but I guess I’ll make it as brief and clear as I can…

First…
Lets look at this chronologically.
1. Yukine’s explanation of existence of light orbs.
2. Kotomi’s parent’s research on different worlds.
3. Akio prayed for Nagisa.

The above proved that… City is magical to begin with. (Keep this in mind)

Second…
1. Tomoya help people out, everytime he did, a light orb appears. (As seen in more than several cases, it’s especially obvious in Yukine Arc)
2. Nagisa’s departure, but Tomoya have yet to receive a single light orb. He wished that he never met Nagisa. (No orb, no wish)(Part one of foot of the hill event… will explain below)
3. Reconcile with Ushio, bawww….
4. Reconcile with his father! Great… to add to that, he receive a light orb, it landed inside him. (Ushio noticed it, Tomoya didn’t)

Hold on…
5. Living with Ushio, living a new life, new reason to keep working hard, for the ones he loved and love.
6. Ushio’s departure, he cried. He suffered a lot, he don’t even know whether he should’ve met Nagisa. (This time, with a light orb, CRAP!)

Lastly…
7. Light orb take him back to the foot of the hill. (The part 2 of foot of the hill event)
8. He would’ve picked “Not meet Nagisa”! HOWEVER!!! By that point, he have learnt that despite the ending he “will” eventually faced, he never regretted meeting Nagisa, he called out to her, and embrace her. “I’m over here”
9. Light orb grant his true wish, to be happy.

After Story’s amazing writing is a double edge sword.
1. Amazingly written sad scene, strongly focus writing.
2. People that are too drawn to the sad scenes may lose sight of what seem to be the minor details. (Yukine’s story and Kotomi’s parent’s research)

In conclusion…
After Story, is an amazing piece of work. The sad scenes were so sad and well written that people forgotten that the town is magical to begin with. And the light orbs are not just there for show. It is only natural for people to not get the show and begin to resent it for apparently having happiness shot out of no where, when in reality, it is all made out to be.

What is really interesting, and I think, an honestly profound notion that the writers of Clannad came up with, is how backwards causation can work in possible worlds. (backward causation explained here: http://en.m.wikipedia.org/wiki/Retrocausality).

First I’ll use an old example to explain this. Essentially Nagisa’s death is like Schrödinger’s Cat. She can either live or die depending on certain factors of the observed future. So what happen is that Tomoya’s wish is granted in this possible future which causes Nagisa to survive. Only when certain conditions are met, his wish can be granted. These conditions come from a notion of Karma that is explained in this story through orbs. Tomoya essentially accumulated enough Karma in both the real and then the possible future to be granted a miracle.

Now there are two wishes that he contemplates. He can either wish to have never met Nagisa, or he can wish that Nagisa survived. Presumably if he wished to never meet Nagisa then he could have caused that to happen. I’m not sure this is the case however. If the world had turned out that way, Tomoya couldn’t have accumulated all the Karma he needed to make the wish. On the other hand if Nagisa lives he can still grant those wished he needs to. It’s almost like he is taking a Karma loan.

There is also the interpretation which I think overlaps with mine, in which there is a metaphor at play. This metaphor is: That the exact moment Tomoya’s child is born, is the exact moment he grows up in an instant. How they overlap is that he is able to keep all his knowledge from the possible world. It’s not clear if he remembers all the details though or just the enlightenment the possible future gave him.