That is a tough one! Season 1 probably had the best writing overall, but Season 3 had the most adorable John and most adorable Rodney and the best John/Rodney moments. Plus you could feel the cast settling in and getting comfortable with each other and their roles. All the team stuff really clicked for me. Season 2 is probably my least favorite, although Aurora and Inferno made me giggly with joy.
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Yay Atlantis!