Considering that this is essentially the mid-season finale, this episode is unusual. The vast majority of the story is set in an alternate Atlantis, where newly created "copies" of Sheppard, Teyla, McKay, and Ronon uncover the mystery of their creation and the status quo of the Asurans, their creators. This eventually leads into an advancement of the overall Replicator arc, but the progress is ultimately incremental.
In terms of the season arc, this episode gives Team Atlantis important intelligence. They are now aware of the Asuran resources (far more than expected) and they have the means to track the movements of the Asuran ships. If nothing else, that should give them ample warning should one of those ships come in the direction of Atlantis. On the other hand, it gives them a true sense of the scale of the Replicator threat, and it is not a comforting thought.
The episode itself, however, is more a meditation on the concept of self. The writers approach two lingering continuity problems with a single plot twist. While the bulk of the Asurans have chosen to pursue the war with the Wraith, a select minority has been continuing to experiment with methods of artificial ascension. To this end, they created "copies" of key Team Atlantis members, built from the ground up and infused with the personalities and memories of the originals.
Not only does this follow up nicely on the first appearance of the Asurans and their concerns about the ability to ascend, but it provides the opportunity to tie up loose ends with Elizabeth Weir. Weir appeared to survive her capture by the Replicators; in fact, it seemed like the perfect way for the writers to slip Weir into the background until a strong character arc could emerge. Instead, this episode delivers a more definitive answer: Weir was killed by the Asurans, and the "copy" is all that remains.
This positions Weir (or, more correctly, her copy) at the center of the philosophical discussion. If the original Weir is dead, but her copy is identical in nearly every respect, does the copy have the right to the same opportunities as the original? And what about the other "copies", all of which must consider the existence of the originals?
Unfortunately, this is too deep a subject to cover in the space of half an episode, so most of these questions are raised with no hope for true consideration. It's hardly surprising that the "copies" are soon forced into a suicide mission to save Team Atlantis from the Replicators, thus erasing any issue of "individual rights". It's a far more heroic end for Weir than an off-screen death would have granted, after all.
Reaction to that bit of news will probably determine one's acceptance of the episode itself. Weir fans will be annoyed that the writers kept options open, only to toss them aside so quickly. This episode gives Weir a relatively strong send-off, given the philosophical heft of the related concepts, but unless Weir's "copy" managed to survive the end of the episode, it's unfortunate that the character couldn't be given a spectacular sendoff.