I understand your point of view, but at the same time I find it curious the addition of the Nevarro Cloning facility plot in the second movie due to the Gideon clones plot of this season. After all, the original reason you took that part out, if I understand correctly, was that it went nowhere in season two. However, this whole cloning plot is not at all relevant in season 3 either. In fact, I think that even if you cut out all the mentions of Gideon’s clones it wouldn’t change anything in this season’s story, because the clones are shown and killed moments later, with no repercussions for the story or the characters.

Of course, with Gideon returning in the coming seasons, these scenes will likely become somewhat relevant, but so far, they’re largely pointless (not that these scenes bother me to the point that I don’t want to see them, I just found it interesting to comment on the subject).