Adaptation issues, Part 1!
In the original LN, there was just one big timeskip - they had the introductory scene setting up how the whole death game started, and then it leapt forward to the "present" where the main story takes place, following things pretty much continuously towards the conclusion of the first big arc at the end of the novel.
The anime took the liberty of showing things in chronological order, which meant adding in all the extra side stories (which were covered after the fact in later novels to flesh things out) right at the beginning of the series. It makes the pacing feel a bit odd.
(I'm not sure how the pacing was in the original amateur web-novel version of SAO, though.)
Adaptation issues, Part 2!
This is what happens when you take separate routes from a visual novel (each of which follows the typical VN structure in which a specific girl becomes the most important thing in the main character's life and the rest of the cast is relegated to side characters as we follow the MC + focus girl's story to a definite conclusion) and then try to fit them all into a single timeline where all the stories happen one after another. It can feel a little...indecisive.
Thankfully this issue is only present in the first series of Clannad, and is almost entirely absent from After Story (which follows a single route, plus a few smaller side stories at the beginning that don't really impact on anything).
