This entire post contains plot spoilers. Also, keep in mind that I played through X. I have no idea how different Y is story-wise, and I can only speak about X's plot.
I was pleasantly surprised with how dark the plot actually got this time around. When I first saw Team Flare I was all like, "Really? Their whole plan is to make a beautiful world for themselves? It's like Team Galactic's Cyrus meets My Little Pony. Great..."
Eventually, after talking to a bunch of random people along the way who provided some backstory and lore and progressing along in the plot, you get a sense that things are much heavier than they appear. A gigantic war happened in the not-so-distant past that nearly wiped out the region. The death toll was enormous (I can't believe they elaborated on that, by the way!), and I suspected that peace was only achieved at the cost of a huge loss of life. My suspicions were confirmed later on. I thought the backstory tidbits were excellently paced for those who were looking for them, and just enough to make things seem grim and urgent and hint that Team Flare's plans were more dire than they appeared. I never tipped those storytellers though. Screw them, I need to buy new boots.
What really got me was, at the climax of the plot when you head out to Geosange to stop the weapon from being activated, Team Flare members prevent access to the route to the south. They mention that they have to just block out the tortured cries of the Pokemon they're stealing the life from. I think that that little line of dialogue is the darkest Pokemon has ever gotten. Their blatant disregard for life kicked my butt in gear and, for the first time ever, made me actually want to beat the evil team. I didn't think of it as a side-plot that I had to suffer through, I was out for blood.
But, it's not all good, plot-wise. I felt that the way they shoehorned in Xerneas was kind of cheap. I felt no connection to the legendary at all. I think that the player needed some exposure to Xerneas outside of the incredibly vague legend we're told all of twice, and before the climax. Perhaps we could stumble onto the sleeping tree Xerneas before Team Flare nabs it? Could the player have been the one to inadvertently lead Team Flare to Xerneas' resting place? I think that would've given the legend some much-needed exposure. As it stands now, Xerneas feels about as legendary as a Rattata, to me at least. Also, Geomancy seems like a move that is easily exploited by whoever Xerneas is facing. I managed to paraflinch it so that it never got the boosts. Xerneas is absolutely cool in theory, being attuned to the earth and life force and all that, but the story made it seems quite flat. Even a small, post-game sidequest where you take Xerneas somewhere to get some flavor lore and a cutscene would go a long, loooong way into making it seem less flat.
In contrast, the climax of Platinum, while not as dark, certainly built up to an epic finale. Cyrus captures three legends and forges a chain out of their very essence to chain down and control the lords of time and space and create a world not unlike was Lysandre was trying to make. Accidentally summoning a being that is powerful enough to rip our world out of balance and destroy us all was pretty damn awesome.
