I've never been one to understand why people want just one game in each Nintendo series per system. I like the games so much that I don't want to have to wait until the next system is released before I get more. Not to mention that, more often than not, whenever a sequel is released on the same system, it is something quite different. Even if it isn't, it's such an improvement or refinement of the previous game (like Super Mario Galaxy 2) that it's still worthwhile.
Things have been like this since the days of the NES. Zelda II was pretty much a completely different game than the first, and to this day I still love it because of that. Super Mario Brothers 3 was huge compared to the original, and Super Mario Brothers 2 was something completely different that I enjoyed. I know some refuse to accept it as a Mario title, but as was stated before, Nintendo has re-appropriated plenty of games over the years. Majora's Mask may have been a "direct sequel" to Ocarina of Time but the only real similarity was using the same game engine. And of course, even more recently, we've gotten both a 3D and 2D Mario platformer all on one system.
What's great about Nintendo franchises is that they are so versatile, as long as fans don't fall into a mindset of what they should be. We can have our 3D and 2D Mario. We can have our first-person and side-scrolling Metroid. We can have our Wind Waker and Twilight Princess. In my eyes, things have never been better.