I realize that 3/4 of these are more suited for TGS, but I'll say them here anyway:
(1) Zelda Wii
(2) Wario Land 5 for DS developed by an In-house Nintendo studio (R&D1)
(3) StarTropics III for DS
(4) Golden Sun 3
EDIT: I agree with DKC4, as long as the development team that takes over the series is careful not to screw around with the formula.