Mistwalker, Grasshopper Manufacture, Rising Star Games (Though I think they're 100% publishers, not developers), Atlus and Access Games.

1. Nintendo
2 Atlus
3 Namco
4 Capcom

Japan Studio
Gust
Media Vision
Nihon Falcom

And of course, Nintendo & Square Enix, but they don't really seem like a fair comparison since they're 10+ studios all under one name while the others are 1-2 teams at most.

Monolith soft ^^

Atlus, Level 5, Namco Bandai.

Asked me years ago I would have said Square Enix and Capcom.

1. SQEX (FF & KH)
2. Game Freak
3. Kojima Productions
4. Nintendo EAD Software Development Group No. 3
5. Omega Force

1-4 were easy, they all make series in which I attempt to buy and play all there games. they are my top 5 franchises ever. i could have split SQEX as it is 2 different teams but that was the easy way. i decided to think of 1 dev who made a franchise that i love and have played for many years but maybe i dont get all there games. that was Omega Force. I only buy the DW series from them and I only buy some of the DW games because I dont need to play them all

Edit: Hounarable Mentions:

Monolith Soft, Gust, NIS, Compile Heart, Persona Team, Tales Team, Tekken Team, Soul Team, Level 5, The rest of Nintendo, Polyphony, Keiji Inafune, Clover Studios, Japan Studios, Chunsoft, Dimps, Amusement Vision, Project Sora, MonHun Team, Platinum Games, Silicon Studio, Yukes, Hudson Soft... ok im going to stop now, although im still missing so many that i love

SCEJ, Atlus, From Software, Kojima productions.

I would have said the same. How things change, eh?

Several Nintendo studios, Vanillaware, PlatinumGames and Treasure.

Sega and Capcom used to be up there...

Everyone of them