Sorry, but it's ridiculous that so many worthy candidates are thrown down because they are "casual." Face it, the fact is that gaming is changing. NintenDogs, Brain Training, and Wii____ are all quite massive hits for Nintendo.
Also, while they didn't establish new characters, Mario Kart and Smash Bros are both big titles. Both are much bigger to Nintendo than Metroid is or ever was. They should count just as much, even if they are recycling a number of existing elements. And of course (as mentioned) Pokemon is a massive deal for Nintendo. Or maybe Animal Crossing which, in only two releases, has sold 2/3 of the entire Metroid franchise's sales (10 games).
Really, the company puts out multiple new franchises every generation and most of them do reasonably well for themselves. A number of them are absurdly good. This question shouldn't even have to be asked.
Oh, and the Donkey Kong franchise is far more valuable to Nintendo than the Metroid franchise, as well, so I can't really understand why you talk Metroid up so much. Doesn't matter much, though, since basically your whole premise is wrong.