There's a much bigger difference in the design philosophy and requirements of Metroid Prime vs, say, Donkey Kong Country Returns. Retro did it anyway. Retro aced it. So could EAD.

Why would you want EAD to make "darker content"? I am curious. EAD is great at producing the main NIntendo franchise and is Nintendo's soul.

Retro is an unusually flexible studio; I simply don't see the evidence to support the idea that EAD have the same flexibility.

I'm not saying I want them to do anything. I'm saying that if Retro Studios was making a sequel to Diddy Kong Racing, I would be perfectly find with EAD, or any of Nintendo's star studios, making a Metroid game in their place.

And Retro didn't have that evidence either. There's no evidence to support EAD's lack of flexibility or inability to make a good or better Metroid than Retro. And they wouldn't need a lot of flexibility. Both are 3D platformers. Both are not heavy on story. Aside level design and art design, there's not much drastically different between the two and like I said; if Retro can go from MP to DKCR, I see no reason EAD can't do the same.

Because Retro is a rare case, it's statistically unlikely EAD is of the same scarce breed.

And you really don't see the vast differences in design philosophy between Prime and Mario? Really?

Retro's not a rare bread. They have four fail projects under their belt. Remember that? They're are just a good studio with talented developers. Same with EAD.

From a game design POV? No. Not other than key differences between the core game design elements in both franchises. You platform. It's in 3D. That's all the similar experience EAD needs to make a good Metroid game. 

Very few devs have the ability to make great games across diverse genres, it is a rare skill.

Where to begin... projectile combat mechanics, much more advanced AI, employing darker content tastefully... so many things Mario is completely unhelpful in preparing for.

Both are platformers. One is 2D. One is 3D. They aren't diverse genres. They're similar genres. Retro and EAD have made both. Metroid is Zelda + Mario + Alien. Exploration + platforming + space. That's all.

Projectile combat mechanics aren't some alien concept that Nintendo had never done before. All Retro did was use Zelda's lock on mechanics and put it in 1st person. EAD could and most likely would do the same. Don't try and say that Prime's AI was even slightly advanced, because it wasn't. It was fun, but the enemies were as simple and predictable as anything in Mario. And I've disproven the darker content bit already, so I won't have a go at that again. Prime didn't prepare Retro for DKCR, but they did it. Not because they have a "rare skill." It's not because they are "flexible westerners." It's because they are professional game designers with degrees were payed to do that. Same would be true for EAD.

You're seriously going to argue that the AI for a Goomba is no simpler than the space pirates in the Prime trilogy? Which is moot anyway as a modern game would be expected to have AI vastly better.

Or that level design is not affected by having to be built around ranged combat, which again would be expected to be more sophisticated today than in 2002?

Seriously?