-Changed the Wraith. I would've made them a bit more terrifying. Perhaps by having them eat humans instead of sucking their life force out. When I was watching the movie Pandorum and saw those creatures, I immediately thought of the Wraith and realized that's what they should've been like. Something like the Pandorum creatures or the Reapers from Blade 2. Not sure I would've had the Wraith be the ones to defeat the Ancients. Maybe left that to the evil Asgard or the Asurans.
-I would've made Teyla and the Athosians more alien-looking. (BTW, I had no problem with Luttrell as an actress and she looked fine to me). But I thought the Athosians were boring and more could've been done with them.
-Done more with the Genii. I probably would've had them be more up front as villains, saving the Wraith, Asurans, and Asgard for special occasions.
-Done more with Ford. I didn't mind how he was mutated, but I wish the character had been more established before he took that dark turn.
-Kept contact with Earth to a bare minimum as the series progressed. By the end, it was too easy to get to Earth.
-Not make Earth the primary target. Earth is almost always the primary target in almost any sci-fi show. So, maybe I would have the Atlantis team trying not only to save themselves but ultimately a group of Ancient descendants or something like that, to remove Earth as the tried and true indicator that something is major on the line.
-Developed Shepherd-Teyla relationship more. At times it seemed to was going in one direction but then the writers veered off. I would've definitely sent them down the path to a relationship, not sure they would've reached it though.
-Would not have killed Beckett off. (When they bought Beckett back as a clone, I would've made him the real Beckett and the one killed off would've been a clone infiltrator)
-If I got rid of Weir (probably wouldn't), I would've replaced her with Woolsey immediately and had Carter guest star as the captain of a starship. I thought Carter brought nothing to the show.
-If not Woolsey as head of Atlantis I would've used Colonel Ellis more or the dude who was Skinner on the X-Files. Though Woolsey would've been my preferred choice.
-Give some non-white people the Ancient gene.
-Built up the evil Asgard more. Included them in the series finale.