The biggest mistake they made was in the premise. SG-1 was an exploration of myth; Atlantis should have been an exploration of legend. Where SG-1 explored Egyptian mythology and Norse mythology and Mayan mythology, etc.; Atlantis should have explored vampire legend, werewolf legend, etc. - everything from centaurs to pixies to golems to trolls. Atlantis should have been Stargate meets Lord of the Rings; but as it was, the Atlantis production team seemed frightened of the idea and always stayed shy of it by creating scenarios that were never explicitly connected to the legends.