Well the Tomoyo Episode was based on the game's Tomoyo Arc, and the sequel game Tomoyo After, so I dunno about it being a fanfic... :P But yeah, watch After Story, hopefully it will expand more, although we'll see. Clannad the game had a LOT of content in it, so I think it was a massive challenge to get it all in.
But yeah, I prefer Clannad over Kanon and Air (and Shuffle!, but that's in a totally different running. Shuffle! is funny and charming and all, but it's basically pornOK, not really :P) for a couple reasons. One of the main ones is probably that Clannad has its happier overall theme, and is more on the light side, as well as it's focus on the importance of family and people around you, the "silver lining" aspect (although this is done a lot more later), perseverance, and happiness in general. Plus, Tomoya has a lot more, well, character, than Yuuchi, or at least, Yuuichi is a lot less memorable. Both where the "player character" in Visual Novels, so character might be hardish to get, but I believe Tomoya got the better end of the stick. Plus I love Mag Mell. I love Kanon too though.