Guy Gardener wrote:
but it would have been grand if it was sexual, and the TPTB were so ignorant about the potential that they left the "possibility" wide open.
Another theory I heard/invented is that Sam didn't like Naomi much because she resented that fact that this changeling (shut up) was a timespace splitted (splat?) widget and not her actual daughter who is probably on ice in a shoe box sized coffin in sick bay.
Her daughter died.
What ever this creature was, sooner or later it was going to go bad.
And who would be better to ease the tension than Our Morale Officer!
Besides that, it's not sure that Samantha rejected Naomi. Her absence may have had more to do with her being occupied with work in the Torpedo and Shuttlebuilding Team. Take also into consideration that we had a Duplicate Kim who was accepted by everybody.
Personally I wish that they would have kept the Duplicate Kes too!