actually, the metroid part of the metroid series is also feeling a tad stale. samus has fought these things 5 times so far, soon to be 6. she's not so much of a bounty hunter. come to think of it, she's never hunted much bounty ever. there's so much more nintendo could do with the character.
however, i think the ganon/link adversary is a little different, because it's not always the same hero. plus, if you think of ganon as an evil wizard who can't be destroyed, it makes sense that he keeps coming back. i don't recall ever hearing that the metroids were indestructible.