Nintendo EAD Tokyo and Kyoto created a game that re-defined the 3D Mario Franchise (Super Mario Galaxy 1/2) while getting some of the highest critical response last generation.
While also being responsible for game changing, audience widening titles such as Wii Fit/Plus and Wii Sports/Resort. Games that, quite possibly, defined the Wii experience for many people. (And spurred many, many knock-offs due to their humungous successes in the gaming industry.)
All in all, Nintendo was great up until the last year/s of the Wii.
However, I don't see any of that pizzazz that you guys see in Naughty Dog. I feel that the Uncharted series became quite bland (which is arguably their biggest franchise.) And yes, I have played them (1 and 2, to be exact.)
Honorable mention would be The Pokemon Co. seeing as how no one listed them, yet they have made many great entries into the Pokemon series all while recovering from the GameBoy Advance blunders. (Even though R/S are my favorite games in the series.)







