I have to confess I didn't have time to read this whole thread (it's pretty darn big!). I think Samus should turn into ZS Samus when she fires her super (as seen in the trailer, if that is her super). Then I also think ZS Samus should have an unique move-set, but be WORSER than normal Samus. Appearently, she's going to be fast, so they should make her REALLY weak, and bad lag time after long-range whip attacks.
So players shouldn't want to become ZS Samus, it would be a drawback for firing the almighty super. And then, when playing as ZS Samus, players shouldn't be able to change back untill they are defeated. Then they start their next life as Samus.