With respect to comparing mobile app store gaming to Nintendo's franchises, I would like to point out one thing:
From its debut in 2009 to last month, the total revenue of all Angry Birds mobile games has been $100m. To my knowledge, no other series in mobile gaming comes close to this. Nintendo's last *single* Mario game, released in November, has so far grossed roughly $230m in five months. The company releases multiple games of this magnitude every year. Their proprietary ecosystem allows them to sell games in this manner, whereas the Apple App Store and Android Play Store has so far not demonstrated the ability to support games which can attain this level of sales revenue.
It seems like a knee-jerk reaction to suggest that Nintendo should move their operations to platforms that so far support far smaller sales potential. Perhaps in the future, the App Store and Play Store will allow for series that sell in the billions, as Nintendo's offerings often do, but they are not yet at this level of maturity, and may not be for quite some time.