Same reason Black/White 2 still released on the ds when the 3ds was already out. Install base.
That would suggest they have no faith in the NX. I think the handheld NX will do very well IF they stop releasing games for the 3DS. If they keep releasing games for the 3DS why would anyone get the handheld NX? Black and White 2 were also sequels to main Pokemon games. They were exceptions, not the rule.
What i've been saying this whole time. No one disagrees a console main pokemon game would be amazing. Nintendo is never gonna do it until the fans STOP buying the handhelds. And that is never gonna happen
All they have to do is port the handheld NX game to the console NX. I'm not asking for a fully 3D Pokemon game with PS4 level graphics. It wouldn't cost much at all and they would make a lot of money off it.
From what little we known about the NX. It looks to be a console/handheld hybrid where the console and handheld parts are sold as separate units. When a developer makes a game for the handheld component it can also be played on the console. This is a genius idea (assuming it's true).
This is why I think we'll be able to play the next Pokemon game on the console NX.