O'Neill's decision in Unnatural selection seemed cruel, but given how dangerous the Replicators were, it was the only good choice available: the Replicators are merged through their subspace link, meaning that technically there are no individuals, so there's no way to know if the guy you're taking with you is the actual Fifth (never mind that they could change their outer appearance) and not First, or literally everyone else. Nor you could know if he could just be overwritten by the others or he has some hidden programming ready to take over in the event their kind is on the verge of annihilation. There were too many unknowns and they couldn't take any chances.
In Atlantis however... OK, the Asurans were designed to be ruthless killing machines, and they made it clear (via Oberoth) that they have no intentions of removing their murderboner programming, so you can't reason with them. But this isn't Oberoth, this is the faction that initially helped them to escape the Asuran city-ship, and most importantly, indirectly gave Atlantis the key to defeat the Asurans and they really wanted to have their programming altered to be more "human". Sure, the circumstances of their arrival to Atlantis aren't the best, but Woosley and the others went too overboard with "the only good Replicator is a dead Replicator". It's pretty clear to me that the writers were really desperate to close the Asuran Replicator story, and the whole "you can't trust nanomachines" was hammered in so that the main characters don't just inject themselves with medical nanobots and fix any challenges they might encounter, thus removing any tension in future stories.
There is however, one giant plot hole that IMO ruins the entire story. The Asuran faction decided to go to some random planet where they would just "meditate" to achieve ascension, as machines. Not even once did it ever occurred to them to:
-Use the Ancient knowledge from Atlantis to build a DNA Resequencer, like the one from "Tao of Rodney" (or like the one Anubis made), assuming they don't already have said knowledge (The Asurans have no use for such tech as they're machines, but there's no reason why they just can't have a copy of the Atlantis database in their "subspace cloud storage", so they should have the schematics for the device), plus whatever knowledge they got from the previous SG missions about ascension and just ascend dammit! Even though that device is found after the Asurans were eliminated from Atlantis, the Ancients already turned it on, and the Asurans would have known about it when they probed their minds. Based on Weir's flashbacks, Niam's faction only seemed to have fled Oberoth after she was captured and allowed to walk free, so they should have had access to all the knowledge that the Asurans got from Atlantis and the Atlantis expedition.
-Even if somehow they didn't have that knowledge, they could have tried to find Atlantis by investigating any of the previously visited planets, it's not like they could get killed by the locals, since they're nigh-indestructible. They could have just eventually run into some Atlantis offworld team, secretly probe their minds and find a way to infiltrate the city to acquire the knowledge from the Atlantis database. No one knows they exist, so no one will suspect them. It's certainly a much better option than sit in the middle of nowhere and hope you somehow ascend.
I guess the writers kind of forgot that the Ancients already had some means of reaching ascension.
Also, was the actress sitting on the table in that flash back really supposed to be Elizabeth Weir? I always thought she was some unnamed Asuran that Koracen was experimenting on and that Weir was the POV "camera man" watching Koracen talking. I can't find any mention anywhere of her being Weir.
Also also, apparently the
ending was rewritten, kind of curious if the original was better.