Did you just watch the first season, or did you go on to see it's second season Clannad: After Story as well? Because, admittedly, the first season is much more generic than After Story, and while the first season had emotional ups and downs (that bit about how your dreams and goals change when you become a parent being a big one for me, even despite the fact I'm not a parent) all the hard-hitting moments that got me to honestly cry were in After Story.
IIRC I saw it all, but it wouldn't be unfair to say that I'm "resistant" to some of that stuff.
The villain in the 2nd half of SAO was better for a few reasons:
- You actually knew who he was and how he operated, because they bothered to develop him.
- He was constantly present as a threat himself, and made choices we actually got to see that influenced the story
- His personality is (subjectively) more annoying. Considerably.
It's debatable whether the "villain" in most of the 1st half is SAO's creator or the game itself, considering its focal point and perspective. Perhaps that's why I found the 1st half more effective though; it told its story very well without having to do a "meanwhile, in villain HQ" type of setting repeatedly. It has the rare case of keeping the present threat level high without actually showing the villain's perspective whatsoever, keeping almost entirely to the main character's, and that does lend to its immersion as you have the same information as most of the characters in the story during most of the series. Adding to that is that they regularly acknowledge the impact of living in a game, and that even if they survive in-game they're still on a timer of sorts (IE their real bodies are lying still).
With the 1st half you had some doubt of most of the character's survival (main characters usually make it, but almost anybody else could have been killed off effectively), as well as when/how the story would end. In the 2nd it was a lot more predictable and the threat to virtually every single person you see wasn't the same. IMO that's why the first half of the series is so much stronger.
(or whatever nickname you personally have for overly-obsessive fans for any of the Big Three).
What are the "big 3" currently? I've been watching more obscure stuff for so long I've kind of lost touch. Naruto and Bleach are obvious guesses; I've seen maybe 1.5 episodes of naruto and maybe about 1/2 of Bleach. Probably not Inu-Yasha anymore, though when I was in college you couldn't put on adult swim without bumping into that (same with DBZ at one point).