"The truth is we were doing prototype tests of Pikmin for the DS and 3DS but it turned into unit management with only the touch pen and no matter what it just didn't seem like Pikmin. We concluded that Pikmin is a game that revolves around action based on its controls and the strategy sits on top that. Although there are elements that are built on the strategy, there are other overall things that have to be well considered. This complete experience is an important elements of Pikmin."
All of which is more than a little vague, but it seems like while Pikmin 3 could've technically worked with the hardware and touch controls, the end result was too far from Miyamoto's vision for the game. Perhaps a portable Pikmin 3 would've required a bit more skill than Miyamoto really wanted for Pikmin 3, which he wants to be considered "a carefree, easy action game."
While other, luckier parts of the world already have Pikmin 3, it won't be released to North America until August 4.