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Hmm. Putting a science fiction character into the skin of a magic-using fantasy character could be interesting... having Samus end up in her home universe with powers that totally do not fit that universe could be very interesting. Which is to say, option one sounds good.
Also, Tharja is creepy, openly stalks the one she loves regardless of their gender, and researches dark magic and curses likely to bring them together, so sending Samus to her home universe to be her twin or replacement via The Portal could lead to all sorts of weird misunderstandings and shenanigans... So that could be good, too. Hmm...
Iblove this idea, I just wish I knew fire emblem a bit better. I basically only got like halfway through awakening before I got bored.