App store development is too volatile to sustain half of Nintendo's business. I don't doubt they'd be able make a place for themselves at the table, but there is too much competition to expect any security. Just look at how Rovio's growth hit a wall when Angry Bird's popularity started to wane. The problem with app store development as of right now is that there's no middle class: either you have a hit, or you have a flop. Nintendo's mid-tier (1-5 million units per title) titles today, such as Kirby, Fire Emblem, hell even most Zelda titles can't exist on the app store because they just don't sell enough to be profitable at a considerably lower selling point. I think Nintendo will have success releasing Pokemon or Mario, but at the same time I also don't think that success will last. Once the shininess wears off, people will move on to the next big thing. That's what happens when you have the largest selection of games on any platform as competition.
Think of it this way: people on GAF look at the Wii as a flash in the pan that was as successful as it was because it was carried by a fad: Wii Sports. From what I noticed, it's generally considered unreasonable to consider Nintendo ever repeating that success, as they "caught lighting in a bottle". At least right now, with the app store market being as unstable as it is, expecting Nintendo, or any developer, to have long-term success making games on the app store is like expecting them to have a "Wii Sports" every year.
