So how long until a misguided mobile effort moves the bulk of the Pokémon fanbase off of Nintendo devices onto phones? When a kid asks for a Nintendo handheld Nintendo should never be giving the parent the excuse to say "Pokémon is on our phone, just play it there".
It's a good point, but I don't think keeping Pokémon on Nintendo hardware would have been sustainable forever. Eventually, some new IP will capture the hearts of the next generation of kids and it will most likely been on mobile (Angry Birds came close, but didn't quite have the legs). This seems like the best move to keep Pokémon alive as long as possible and still make money off it. Besides, it may force Nintendo to go for something new...and I'm totally OK with that.
Also, parents will always say to their kids, "you have games on your phone, just play those" regardless of the situation.