Xenoblade, the first game has so many creationist and religious themes, and the second one well... its start with the earth been destroy it.

Didn't we just have this thread a week or two ago?

We did, though that time I think it was "darkest game", not franchise.

Subtly, Pikmin. Rightfully, Metroid.

Twilight Princess is also pretty dark. They forgot to push the "colours and lighting" button

Darkness isn't really determined by killing off a whole bunch of people off screen; if it was, then the "refusal" ending of Mass Effect 3 would be the darkest moment in gaming history. Games that are dark are usually ones with heavy atmosphere, death/destruction that you physically get to witness/observe, and characters that the player feels attached to being killed off/hurt in some way. As a practical example, Apollo Justice: Ace Attorney is a much, much "darker" game than Dead Rising, despite the fact that millions of people die in the latter and a grand total of five people die in the former. Death means relatively nothing if we have no attachment to the characters who die in the first place.

Pikmin. It's a franchise about slavery, racism, and genocide. It's basically a reenactment of the colonial era, where technologically superior beings show up, force the natives into bondage and work them literally to death in order to stripmine their land in pursuit of material wealth.

Metroid as well. Super Metroid's title screen had human corpses on it, while the opening of Prime is grim indeed, as you explore the wrecked space pirate frigate, first finding mangled bodies whose cause of death your scan visor recounts in gruesome clinical detail, then later wounded and dying pirates whom you gun down as they try feeble to attack you, while your visor informs you that "this subject has suffered severe haemorrhaging of the brain, and therefore cannot aim effectively" or "subject's legs are broken, preventing it from escaping".

Prime 2 similarly details the emaciated corpses of Luminoth warriors who stayed at their posted until they starved to death, or killed themselves to avoid being possessed by the Ing. It's atmosphere is also deeply oppressive; brilliantly so, but so much that I actually found long play sessions exhausting.

Nintendo sorely needs to revisit this kind of territory, it would bring some much needed variety to their first party catalogue.

And here I thought it was just an analogy for Huffington Post's relationship to political reporting.

Oh wow, you just reminded me of that. I just love how they had a real reason to be there. They didn't just put them there for visual decoration; they have a story, feelings, even families some of them. 

That's one of the greatest strengths of the Prime trilogy as a whole in my opinion; pretty much every part of the world feels thought out and cohesive.

Definitely Metroid.