It is never implied that Eike could be either a descendent or Wagner. This is impossible, even if we are traveling through different timelines. There are several constants. So if Margarete is most assuredly not his ancestor, why does Homunculus expend so much energy switching her with Dana?
1. Well to take advantage of time's "homing instinct" as he calls it. He knows time will try to sort them out, and indeed Dana does get sent to the past with Eike, drawn to him with the stone. This is the only way Homunculus can get the stone to Wagner/Eike without contacting it directly.
2. Merely to reassure Eike. At any cost, he cannot have Eike chicken out at the last minute, so he does this merely as a reassurance to Eike. He also misled Eike as to who his ancestor was so that his real ancestors would never be in danger.
3. He's a total jerk! He gets pleasure out of causing Wagner pain, even if Eike is not able to understand why this is so personal. Look how delighted he is in any ending where Wagner/Eike accidentally kills his own son. He is sadistic. He is also positively delighted when Eike brings Dana back to the present, the only ending he doesn't politely remind Eike to return his guest to the past, knowing she doesn't really belong there and that they may commit incest together. He is proven to be dishonest and cruel.
4. I wrote these here by accident, but would still be interested to see other reasons for his switching them. It seemed to accomplish the three above items but also enable him to conceal his plans and what he had done to Wagner.
Edited by Kangar00spy
How do all the Paradoxes exist?
My apologies, I wrote these in the wrong section and can't seem to delete them. Still a good discussion question though!
Edited by Kangar00spy