Skyward Sword was good overall (even if disappointing) while Other M was mediocre gameplay wise and terrible story wise.
Zelda is generally better, though Metroid won on the Gamecube (MP1 > Wind Waker > MP2), tied on GBA (Zelda: Minish Cap and Metroid Fusion) and tied on SNES (LttP and Super Metroid are equally amazing). For Wii, if you count Twilight Princess (otherwise, I consider it better than MP2 but worse than Wind Waker for Gamecube), then Twilight Princess = SS > MP3 >>>> Other M, so Zelda won on Wii,
That's from a quality perspective, but from a sales perspective, Zelda has almost always been superior. Metroid Fusion slightly outsold Minish Cap, so that's one win for Metroid, but the GBA ALttP port out sold all Metroid games on GBA combined.
