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.
That would have been an interesting concept...wondering how that would fit in terms of earthlings being exposed to them, however, and starting the legend.
i would imagine that there would be some time traveling in addition to the travel from Pegasus...