I think this episode is one of the best I've ever seen, really. It ranks up there with SG-1's Heroes. Yes, there are similarities, and anyone who remembers watching Heroes when it first aired will notice them. But it's also vastly different. I don't want to put any major spoilers in here, but I think fans of both series will know what parallels I'm drawing with the mention of Heroes.
I'll say this: It was a fitting episode, and one not likely to be forgotten. Not everyone is going to like it, some are going to hate it outright, and a few will probably stop watching altogether. But Atlantis is going strong, taking a darker turn, and maturing as a series. She's finally stepping out of her big brother's shadow.