Nintendo will develop the games, Miyamoto's probably not involved (yet) and it doesn't sound like free-to-play's the way forward. Nintendo's boss Iwata has plenty of new info to reveal.
Firstly, it looks like most of the work will be done in-house with Iwata stating that "development of smart device games will be mainly done by Nintendo". The DeNA partnership is mostly about its experience with mobile gaming and "the 'service' side of things". According to Iwata, its new partner "will be primarily responsible for the service-oriented operations" and the collaboration is intended to "greatly leverage strengths of each party". As an additional bit of info, he mentions that Shigeru Miyamoto isn't currently involved ("his priority is on the development of Wii U titles that will be launched this year") but that his involvement is up for discussion "when possible".
In terms of pricing models the key thing for Iwata is "how we can get as many people around the world as possible to play Nintendo smart device apps, rather than to consider which payment system will earn the most money". He talks about how free-to-play is more widely adopted and is an option, but that pricing will be discussed for each title. There's mention of not wanting to hurt Nintendo's brand or IP, and finding a model that "parents feel comfortable letting their children play with".
As for why it took so long to get involved, again the idea of not hurting brands or IP is mentioned (it's an ongoing theme in the interview). Iwata mentions the idea that "in the digital world, content has the tendency to lose value, and especially on smart devices". He adds that maintaining the value of Nintendo's content is partly responsible for what he calls "our careful stance". Whatever he has planned, it will be "new software which perfectly matches the play style and control mechanisms of smart devices".