>>2146852I suspect because it's not canon, anon. I often have the same problem with harem anime (dunno if I'd necessarily call Clannad harem, but I digress). Always feels like the main character doesn't pick the best girl, as far as I'm concerned.
Maybe you're the same way?
At any rate, I suggest playing the Clannad visual novel if you haven't already. May help you out.