So generally I feel this is a slam dunk for both parties.
On Nintendo's side, they're likely getting some ridiculous royalty like 35-50% of the money made after Apple/Google take their cut.
DeNA is a prominant, long time Japanese mobile vendor that specializes in adapting licensed IPs into successful games that are well tuned for mobile audiences, and have had some good success overseas. While they were most prominent in the feature phone days, they do still have modern successes in Japan, have some remaining success in the West, and with the strength of IPs like this, should be able to make very significant launches that both acquire and monetize well. There are very few companies that have success both domestically and abroad in mobile, so this is notable.
Given that mobile now dominates the casual market, holds great sway over children, and is the dominant form of gaming in many emerging markets (and even Japan for that matter), Nintendo will also get their brands in front of many more people, which makes them much more valuable as licensable IP for merchandizing and transmedia efforts. It keeps Nintendo's IPs relevant as well in world where handhelds are fading and Nintendo's consoles are borderline moribund.
As an even further bonus, the type of games that succeed on mobile have very little overlap with those that work on handhelds, so for the short and mid-term, Nintendo can keep on making handheld games without hugely fearing cannibalization. Obviously there will be some amount of cannibalization, but given how much handheld retraction has already happened, Nintendo might end up gaining as many new converts as they lose to people who are happy to just have a Mario autorunner on their phone. In the short term they could even grow a bit, though I think the long term prospect is still a steady decline. With the NX account system, they can try and encourage this as well by doing things like sending Pokemon to your 3DS/4DS game box by achieving certain things in Puzzles & Pokemon or vice versa, which helps entice people to play both.
On DeNA's side, this is quite possibly the biggest licensing deal in mobile history. Nintendo's brands are extremely well recognized and incredibly popular, and people will flock to them on mobile in droves. Given that DeNA already has monetization down pat, this should result in a windfall profit. This also gives them a great avenue to worldwide relevance instead of earning overwhelmingly from Japan. Acquiring all these new users to their platform is a great way to boost their other games as well. Beyond that, assuming these games are successful, which they almost assuredly will be, it also gives them a great sales pitch for licensing more IP to boot.
For Nintendo, I think the next step is working hard on getting great licensing deals going for TV, cartoons, and film. Disney, Warner (Cartoon Network), or even Viacom (Nickelodeon) would be good partners. This will get their brands in front of even more audiences, especially kids, and help them try to remodel the company into an IP and merchandizing powerhouse, which feels like a much stronger direction for the company. They can obviously keep video game development as one of their strong arms of the business, but they desperately need diversification, and this is the most straightforward and obvious route by far.
