Prior to Nintendo EPD, the division that handles all Nintendo development and publishing for the Switch, Switch 2, and Mobile. Nintendo's first party development was split between the EAD division, the legendary group of in-house studios led by Shigeru Miyamoto, and SPD, which while did some internal work, was primarily a group of publishing units that managed and oversaw the development of games made at external companies, including overseeing Nintendo's subsidiaries like Retro Studios. 

This structure lasted from the start of the Nintendo DS, all the way up to the end of the Wii U, and both divisions pumped out a lot of titles in that time span.

Notable EAD games and franchises:

Super Mario Galaxy 

The Legend of Zelda

Animal Crossing 

Wii Sports

Nintendogs

Wii Fit 

Big Brain Academy 

Mario Kart

Star Fox Command 

Flipnote Studio

Splatoon

Nintendo Land

Super Mario Maker

Notable SPD games and franchises:

Pokemon (The Pokemon Co./Game Freak)

Super Smash Bros. (Sakurai/Sora)

Metroid Prime (Retro Studios)

Donkey Kong Country Returns (Retro Studios)

Fire Emblem (Intelligent Systems)

Rhythm Heaven 

WarioWare

Brain Age

Xenoblade Chronicles (MonolithSoft)

Sin & Punishment: Star Successor (Treasure)

Mario Strikers (Next Level Games)

Pandora's Tower (Ganbarion)

The Last Story (Mistwalker)

The Wonderful 101 (Platinum Games)

Style Savvy (syn Sophia)

Between this output each, which division did you think did the best?

I'd actually say this is closer than one might think.

The big guns like Mario and Zelda are obvious wins for EAD, but on the other hand the SPD category also produced some of the best Nintendo titles of this era such as Metroid Prime 3, DKC Tropical Freeze, Sin & Punishment Star Successor, and Xenoblade Chronicles.

This is a bit misleading as its well known that developers rotate across different teams in the company to bring new ideas to other franchises and gain new skills and insight, the same group of people could have worked on games in both divisions.

EAD by a landslide, imo.

My two favorite Mario Games and My two favorite 3D Zelda games released by EAD on Wii.
The only game I felt it was worth owning a WiiU for was Mario Maker, EAD again.
On the DS I mostly played games from other developers, but I did like Wario Ware and Brain Age more than for example the Zelda titles on the system. I also think it was the best time for pokemon with Heart Gold/Soul Silver and Black and White. So SPD take it.
3DS Had a good (original) Zelda and a good Fire Emblem. But I never liked the system very much. Probably played more Fire Emblem Awakening than Link Between worlds so I give it to SPD.

Conclusion EAD for stationary consoles and SPD for handhelds. But over all with the dominance of EAD for the Wii I think it wins.

Thing is, I mostly played games from SPD and their partner studios so the Win's gonna go to them but that's because I spent on the DS mainly.

Galaxy games are enough to tip it toward EAD in a pretty competitive head to head. EAD had the better home console titles and SPD had the better handheld titles.