Cutscenes probably won't show up until we're well into a 3DS game. (Rendered in 3D!) I'd actually like to see that approach. I'd also like to see voice acting, and I bet that'll be on a potential 3DS game too.
Rendering cutscenes for two different protagonists isn't that bad. See Fire Emblem Awakening, where there's a very large combination of characters you could potentially have; the various combinations of attributes would be impossible to create cutscenes with.
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