Thank you for the context. Even though the two divisions are now under one umbrella, wouldn't it be reasonable to think that the old hierarchy's imprints would lead to games following both development philosophies? Or are you expecting the merger to mean that the two divisions fully meld together in their output instead of simply just be grouped together for organizational structure?
In a way, yes. While several EAD mainstays are still in EPD such as Yoshiaki Koizumi, Katsuya Eguchi, and Ejji Aounuma. EPD also inherited SPD and R&D1's figureheads such as Yoshio Sakamoto, Ko Takeuchi, and Kouichi Kawamoto. They joined the aforementioned EAD posy in high positions within the division, and are able to share their ideas and philosophies with the EAD programmers and artists they work with, as well as vice versa. So we'll get games of both styles. My main point was that the old R&D1/SPD guys now have access to EAD's legendary talent pool, allowing them to be more ambitious with their projects than was possible before, which in turn, can lead to more stylish, unique, and weird, even by Nintendo standards games.
The biggest change in my opinion, is Miyamoto stepping down as General Manger, with Shinya Takahashi taking his place. This is a key difference because the philosophy in which these two manage developers couldn't be anymore different. Miyamoto always had very specific views on games, while he was an incredibly creative and talented designer and game maker, he also knew how to make blockbuster hits, and were able to make games that were very marketable and easy to grasp. He shared this talent with the many designers and creators he's worked with over the years. And while they give Nintendo's games a cohesive aesthetic, they also come with the side-effect of feeling slightly homogenized. Takahashi on the other hand, takes a different approach. Rather than share his philosophy with other designers, he instead focuses on cultivating each developer's unique talents and identity. The best example of this difference in philosophy, is Wii Play vs its sequel, Wii Play Motion, which EAD and SPD developed separately. While Miyamoto gathered a single team to come up with mini-games for the Wii Remote, Takahashi instead brought in a dozen or so external developers, and asked them to each make one game, in their own style. The finished games would then be complied into the final product that exists today. If you want to know more about the development of Wii Play Motion, check out the Iwata Asks interview, it's really interesting.
Basically, while Miyamoto encouraged unity, Takahashi encourages individuality, and that key difference is what's going to shape Nintendo's first party output going forward.