XY overall theme was life and death. There are many scenes where the player got confronted into that theme and they even mentioned that someone died. And the whole TF plot was also pretty much "kill everyone except us" thing.
Also I can't see why Gen V was darker. DPP storyline with Cyrus and his suicide was already more darker than "let's free the pokemon of the humans and then we abuse them like every Team Rocket".
I think people feel that BW was a darker game because there's just more meat to the story than in the others - N in and of himself is a tragic story, you have themes of betrayal coming with Ghetsis, more mature characters, etc. Though I agree that XY and ORAS had more obvious dark parts, BW is far subtler, and I prefer that rather than the in-your-face gloom.
Yeah, what I mean by my earlier post about Gen V being much darker was that, yeah, Gen VI's whole deal was life and death buuuuuut... it was almost cartoony in how it was dealt with. Team Flare's goal was to "kill everyone except us, maniacal laughter followed by an awkward pause as they figure out how to actually
do that". Like, okay, you made a big crystal thing come out of the ground, and apparently it was used as a nuke laser in the past, but even as I was at the climax of the game, there never was any threat of menace. Like, Lysandre just seemed like a rehash of every sympathetic anti-villain trope until he went off the deep end, and that just seemed kind of contrived. Sure, there were references to death and dying throughout, but nothing more grim than what we got in the Canalave library? I mean, I don't think it ever felt
real to me, that Team Flare posed a real threat. Sure, they took over a power plant and a factory and harnessed a legendary's energy, but that's what Pokemon villains
do. It felt like they were just going through the motions.
Even in ORAS, Maxie and Archie are always just sort of in over their heads. And in the Delta episode, Zinnia's backstory is too all over the place in an attempt to make her edgy and mysterious for me to take it all that seriously.
But in Gen V, you got a sense of what Plasma's goals were. A lot of the grunts genuinely believed in the justice of what they were doing. N and Ghetsis and Colress were fleshed out characters, and even some of the sages got some good development in BW2. N was, as stated, a tragic figure that you related to, and the climax where you fought your way up the castle seemed
climactic, because as you did so, you were learning just how completely messed up N was and how Ghetsis had conditioned him that way. Ghetsis presented a clear and present danger to the region, and there was nothing cartoony about him at all. In BW2, he is perfectly ready to kill the player specifically, not the vague threats that other leaders made. Even Colress was scary, in a morally ambiguous type way. Not to mention that Gen V did a really good job of illustrating anxiety about growing up, moving past loss, dealing with troubling family situations, etc. I don't know, I guess I just felt like there was much more at stake in Gen V and that lent the plot urgency, like the actions I was taking mattered to the fate of the region, and that drove home how dark things could have turned out had the player not gotten involved.