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iamserious said:

It is not a very big seller. It is a good franchise but it isn't one that will increase sells so Nintendo is focusing on games that will (Super Mario, Smash and even Zelda).

Nintendo has always focused on Mario, Smash and Zelda and yet they were still able to produce good quality Metroid games. Besides, Super Mario 3D World barely pushed the sales of the Wii U and Smash doesn't seem to do much either considering we're in the Holiday period. 

Personally I think Zelda and Metroid are very similar games, only Metroid is far better. Better story, better graphics, better puzzles (that aren't re-used over and over again), better bosses, better item upgrades and better use of said items in the overworld (in Zelda you only use a certain item in a specific dungeon, after that it's practically useless). It's surprising that Zelda is so much more popular than Metroid. 

I guess Nintendo just didn't care as much for Metroid given the fact that the maker of the franchise left Nintendo (and died shortly after).