I just finished watching the third season DVD set, and while Stargate Atlantis is still my favorite Sci-Fi show, I was rather disapointed.
(Warning! Spoilers below!)
First, story arc failure. I was expecting a huge advancement in the story arc concerning the Wraith, but it just didn't happen. Sure, they appear in a few good episodes, but it didn't seem like the story with respect to them in particular moved at all.
Second, killing off Dr. Beckett. I really liked him. Maybe I'm dating myself a bit here, but he was kind of like Scotty and McCoy rolled together but with a cooler head. This very lovable character will be missed.
Third, rehashing the replicators. With an entirely new galaxy as our backdrop for this series, why do the replicator thing all over again? It was original enough on Stargate SG-1, but I was amazed that Atlantis started a story arc with replicators too. Are they going creatively bankrupt already?
Fourth, rehashing old sci-fi standbys, like the "weird alien thingy or disease that causes loyal comrades to start killing each other". Did the original Star Trek do this in the episode "The Naked Time" and wasn't it done again by Star Trek Next Generation as the second or third episode in that series?
Fifth, bringing back a whole ship full of "ancients" just to kill them all off by the end of the two part episode. So, the "ancients" have gone from being a great and mysterious race of humanoids from the past to an expediant plot device. We can create them and destroy them at will just to get and episode or two. Couldn't an "ancient" or two have been spared and used as secondary characters? Wouldn't that have been interesting? They could have helped explore the rest of the city. Their ship could have been recovered. There's so much that could have been done with them that wasn't.
Sixth, lack of character development. Tayla could be a full-fledged warrior princess with a rich heritage and tons of wisdom, but she seems little more than a pretty (to say the least) face with a great body who never uses contractions (reminds me of Barbara Eden in I Dream of Jeanie) and tilts her head a lot. And then there's Ronan the Monotone Macho man who does nothing for me but must appeal to a certain demographic so he's still there.
Still, the season ended with a special effects spectacular and a tightly written script that showed just what the Atlantis team is capable of. And, of course there's the wealth of special features and commentaries that you get as part of the standard package with Stargate franchise DVD sets, and that greatly adds to the value of the set.
I haven't seen any of season four. Here's hoping.