Which is really refreshing from the usual "I'll change the main character to one from the story I chose, or to my self-insert, and show how awesome they are without changing any scenes" which gets somewhat annoying as soon as the so-called butterfly of doom ought to start changing things due to different outcomes of past scenes. A fun example are people who write "Zero no Tsukaima"/"Familiar of Zero" fan fiction in which their inserted character was capable of helping Louise with her wedding speech, and yet they still go adventuring because the author has no idea how to build on situation in which they wouldn't get the zero fighter and the initial invasion succeeded, even for just some time, due to Louise not being present in the village of Tarbes at the time.
Well, it's not that hard for me to actually make that choice. But then again, I can be a genuine sadist when it comes to characters in my stories (one of the stories I'm currently writing does end with the main character being utterly broken and going over the morality horizon because of that).
But if you asked me, I'd send the original three, with Ilya, leaving everyone alone. And then do it again and use the problems of Galen becoming concerned due to the supposedly never-ending jumps, Takara becoming concerned with well-being of her family due to less of its counterparts being present in some universes, and Ilya becoming afraid to form a family again and Shirou having to deal with it (and not exactly succeeding at first). But then again, you aren't likely to go into that direction and I already stated I'm a sadist when it comes to that sort of thing so taking my advice is likely a bad thing.
Well, that is true...
Sorry about that - it's hard to divide it if it's all just one sentence. But I'll try to be more merciful in the future.