No they didn't. The Milky Way replicators started off as replicator blocks and consciously decided to evolve into a form like their creator (Reese) in order to correct an error in their programming. The Pegasus replicators started off as nanites and followed a program to turn themselves into the ultimate weapon to fight the wraith (the Ancients).

The Milky Way replicators viewed the more human-acting replicators as defective, while the Pegasus replicators actually strive to be more like the Ancients (even to the point where a number of them want to ascend).

This is possible but nowhere is it stated that the replicators actually use the same technology. ARGs disrupt the "energy" that holds replicator blocks together, but evolutionary convergence means this is a rather meaningless observation. The Milky Way replicators were designed to use this energy from the beginning, but there is no on-screen evidence to indicate that the Pegasus replicators were ever intended to form into macroscopic objects. In fact, the Ancient scientists expressly did not intend or expect their creations to adopt a humanoid form at all.

The Dakara Outpost is also a meaningless point, since the machine itself was designed to terraform other planets in the Stargate network very quickly (its life-destroying and replicator-disrupting capabilities were programmed into the machine manually). It was also built millions, if not hundreds of millions of years before the series.

I think the series is going well so far. I'm really glad they've picked up with the pace of the episodes instead of filler ep's here and there. The series feels much more focused because of that, and I like the way they're exploring the characters more.

But I fail to see the point in Carter's appearance in Atlantis...

She's supposed to be running the city now that Weir's gone, but I don't see much evidence of her actually running the city. She's missing from too many episodes - enough to make it look like Sheppard is running the show. Most of the major decisions that should have been made by Carter has been made by Sheppard. I think she could be a great addition to the cast, but they have to start using her character better.

The main thing that made it obvious to me was the last episode, "This Mortal Coil" (spoilers follow).
The vision that Sam was shown in "The Seer" became reality in this episode. Why wasn't she involved? Also, "Weir" came back and at the end of the episode they were talking about moving her belongings back to Earth. Since Weir was her predecessor, I'm surprised they didn't work her character in the scripts...

I really like where they're going with this season. I just hope they can keep this up for the rest of this season and into the next!

Carter is in eight of the final ten episodes and should be getting more screen time. She was working on the SG-1 movies when the first half of this season was bing shot, so her time was limited.