It's always challenging to answer this question, due to variations in developer size, and the fact that it's sometimes difficult to distinguish individual design teams within larger studios. I think we need multiple developer tiers, for example small, medium, large, jumbo, etc.
That being said, it's Nintendo EPD, formerly Nintendo EAD, formerly Nintendo R&D4. This game development dynasty has produced (and continues to produce) so many masterpieces that's it's just absurd at this point. Its best game: Breath of the Wild.
In second place, I'd put Capcom's Consumer Games R&D Division, with a special focus on Development Division 1. Overall, I think Capcom is the only modern entity that can compete with Nintendo in terms of software quantity & quality.










