Must be all that processed meat...  

Bu...bum bum....

Naughty Dog actually has a LOT more behind the scene influence and relevance for Sony than many of you are either realizing, or acknowledging.

Sonys ICE team. Their technical aces, the top notch team that developed the creation tools for PS3. The guys that laid the framework for development on CELL. Led by core members of Naughty Dog.

Insomniac Games - creators of Spyro the Dragon, an IP that was exclusive to PlayStation at its start, creators of Ratchet & Clank, etc... They were next door neighbors to Naughty Dog. The two teams shared technical knowledge and helped each other out. They were literally sister studios and its obvious that Insomniac was heavily inspired by Naughty Dog. During the PS2 era, a triplet was formed - sucker punch. This is another team that was directly influenced by Naughty Dog. Ever wonder why Jak & Daxter, Ratchet & Clank, and Sly Cooper had a similar tone? These three studios worked closely with one another and without ND leading the way, there would be a remarkably big hole in Sonys first party lineup.

Without Naughty Dog, who would've proven the Cell? What was the first truly stunning AAA PS3 game? Like I said, Naughty Dog has and continues to be a significant chunk of framework holding PlayStation up.

Bungie did one thing for MS - Halo. Which wasn't even going to be an Xbox game (originally targeted for PC/Mac). That's literally it. Just Halo.

Naughty Dog has done way more for Sony, they've built engines used by other devs, they've worked closely with other studios developing their games, they've only gotten bigger and better with their 1st party releases and well... They're still a 1st party team.

This x1000!

Naughty Dog, one of the smartest things Sony has done. Also Sega buying Atlus, Atlus may be Sega's only hope.

From a standpoint of best games being produced, Retro Studios.

From a standpoint of profitability, probably Rare or Naughty Dog.

Retro is a good one, they essentially tried to fill Rare's shoes during the Gamecube era and did to a large extent with the Metroid series, however I don't think they are prolific enough as of yet, especially considering they only have 1 game out for the Wii U(maybe 2 by the end of its commercial life).

Monolith Soft. Both companies has helped each other out, an aquisition couldn't go better than that.

Because of Monolith Soft, Nintendo is better and because of Nintendo, Monolith Soft is better.

KojSoft

This will be the studio created by Hideo Kojima.

Sony will snap the studio up in May 2016 where Kojima will pledge to release his game in 2019. At E3 2018, his project will be announced and is an emotionally deep open world RPG about life (Project: Deep Blue Ocean). PS5 is announced early 2019 and at E3 2019 project deep blue ocean will be officially called "Existence". The game will be moved over to the PS5 and with a release for the launch of PS5. PS5 will launch in November 2019, Existence will launch May 2020.

So I will have to go for Sony's aquisition of KojSoft and Kojima's critically acclaimed RPG.

If you want my honest opinion, and not just me regurgitating things I plainly don't care about...

I'd think it's Atlus.
I wouldn't care about Sega - at all - if Atlus wasn't under their care. They could very well guide Sega to a better future in terms of software development and localization.

A close second would be Monolith Soft, if they developed titles faster, that is. Their philosophy is actually really compatible with Nintendo - especially with the top brass - and I think they could very well guide Nintendo to a brighter future. They're already working with third-parties like Bandai Namco (though only PxZ has come of it...they should do more, like Xenosaga HD collection?), assisting other first-party studios (see their assistance with The Legend of Zelda for Wii U), and they've blazed forth with a new genre and lead IP for Nintendo (open-world RPGs, and Xenoblade).

Though, I'd be inclined to agree and regurgitate what others have said in this thread.

(Massive levels of opinion incoming)

At least, in my personal opinion, despite having a limited library to work from, I've enjoyed Retro's titles more than any other second party developer. The four other big ones that stand out in my mind would be Bungie, Naughty Dog, Rare, and most recently Atlus. I'm not a huge fan of RPGs, so Atlus gets knocked out quickly. The Halo games are enjoyable, but they've never entertained me past being dumb fun. I've never really enjoyed the Uncharted series, and while I thought Last of Us was a good game, I don't think it was a great one. That leaves Rare, and while I certainly enjoyed the heck out of a number of their titles (DKC1&2, Killer Instinct), the rest fell back on fetch quest style in increasingly wacky environments, and while I find a lot of Rare's creations to be enjoyable games, they're not what I would consider being great.

The Metroid Prime titles, meanwhile, are all games that I'd place in my Top 50 of all time list, easily. DKCR and TF were about as enjoyable as DKC1 and 2, only with the added benefit of co-op that made it even more fun to play. Retro's lineup is definitely limited, but they've hit the ball out of the park on every single title to the point where I think I'd take playing their 5 games over any of the aforementioned four's entire library.

Admittedly that all has to do with solely the perceived quality of games. If we are talking about how profitable they were for the company they're owned by, then yeah, Retro loses big time to something like Rare, Bungie or Naughty Dog.