I figure the reason why that won't happen is that kids will find themselves with two, say, Omanytes, one as a Stage 1 and the other as a Basic... so when you have something like Omastar which could be a Stage 1 or Stage 2, which one would you put it on?
Obviously Stage 1's can only go on Basics and Stage 2's on Stage 1's, but that doesn't mean that people won't be wigging out about it.
But don't get me wrong, I've always felt that switching the stages like that was the only way to make them (and other cards) feasible. Case in point, I think it's silly that, in the TCG, Pichu (and other Baby Pokemon) can't evolve into Pikachu, etc, unless they specifically state so with a Pokemon Power. Silly!
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http://www.fakecard.com/fakes/pokemon/mayakashi/images/145-smoochum.jpg
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http://www.fakecard.com/fakes/pokemon/mayakashi/images/074-jynx.jpg
But anyways... there we go.