You mean the controls, or the whole game?Doubtful. I don't see devs wanting to limit themselves severely by moving to the 3DS. It's not even half as capable. Plus the design has to be pretty different to fit the 3DS style.
Becuase.. Circle pad pro..
Not so much control layout (though I remind you the CPP is a clunky "optional" addition and games can't require it as of yet), but just the dual screen vs single screen is a huge difference. Sure the Vita has a touchscreen now, but I doubt it's going to get as much serious attention as the DS does. It can be a pretty awkward transition, though i'm sure some games wouldn't be hindered by it aside from the actual capabilities of the handheld itself.