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Well, I think you come up with some good ideas. The "which shop in the bazaar" lists weren't quite as compelling, but ones like this have been worthwhile.
I kind of like fatesplit types of episodes, personally, as they enhance the "choose your own adventure" aspect of the story.
Option 3 is exactly the sort of thing I was thinking of when I asked if you'd be doing a list. Rei impregnating Asuka? Fun. So the baby would be 1/4 Lilith, 1/4 Yui and 1/4 Kyoko - and therefore possibly capable of piloting all three Units, if she were her parents' age. That could always happen later if someone put something bizarre in the WP. Or it could make Asuka capable of piloting them all while carrying the baby. Alternately, it could make it so that she couldn't pilot any.
If option 5 happened, Gendo would just get rid of Rei and bring out a new one. And if that didn't work, he'd probably get rid of Asuka instead.