The problem with XY's Flare plot in regards to Lysandre's plan is that is was split into two though the plans didn't change. Lysandre's plan was always the same: use the Ultimate Weapon to make the non-Pokemon members of Team Flare immortal and kill everyone else. However depending on what version depended on the power source of source of the Ultimate Weapon. It's implied it doesn't matter what the power source was, Xerneas or Yveltal were just a battery. Honestly, Xerneas being the life Pokemon and Yveltal being the death destruction Pokemon doesn't really play a part in the story at all, it's just that Lysandre focuses on the Legendary's aspect of mortality because it's on his mind. But anyway, the game doesn't really tell you this causing a sort of problem in both version's story:
X: How does Lysandre plan to kill everyone with life energy?
Y: How does Lysandre plan to make Team Flare immortal with death destruction energy?
Without assuming the Ultimate Weapon can transform the energy, you're left confused how Lysandre is going to accomplish half of his plan.
Who knows if Z was going to fix that. If it was a traditional third version than they could have easily combined the plots. If it was a sequel paired game they could just clarify the Ultimate Weapon's use of energy.
BACK ON TOPIC!
So something has been bothering me. The Ultra Poke Ride looks to be an important mechanic, yet Nebby gets taken over by Necrozma after becoming Solgaleo/Lunala. So how is this going to work? Is Ultra Poke Ride going to just be a post game thing? How do we get to the Ultra Recon Squad's world than?
Which is basically why XY's plot is filled with all sorts of glaring holes that are soreful to watch at. But from my understanding, while Xerneas' and Yveltal are practically bigger batteries, Lysandre just said he will spare all members of Team Flare and blow everyone else up, and maybe it is just a fluke - After all, if everyone including himself is dead then who can prove his words anyway?
X: Probably just like heat and electrical energy, Life energy is also a form of energy which he converts into something ultra deadly (say a very condensed energy beam like a Hyper beam). Maybe it works like Getter Radiation from the Getter merchandise, which sufficient amounts of radiation enhances evolution, but more than that is gonna turn you into juice. Or otherwise, it's just a special form of energy while can be super powerful as a weapon, it can also be used to grant life.
Y: Similar to Xerneas from above, but not directly the energy generated from the pokemon itself, just stole it from it's piggy bank. It doesn't mention anything about granting life to anyone (unless my memory is shoddy), but if Yveltal maintains lively by absorbing life energy, maybe that can be done in reverse. After all, TF managed to drag out its life energy to fuel the cannon, I guess it isn't much of a problem to give it to others, should it really be meant for life to prosper.
Some ground-breaking stuff occured my friend. Remember there is somebody talking about the Rainbow Team Rocket thing which most people debunked it as fanfiction? It's actually TRUE, of all things.
Take note at the rainbow coloured R under Decidueye, and the two members that have a rainbow-themed background along with their typical team Rocket clothings. GF surely pulled out all the stops this time, but again Lysandre became a problem. (how is he still here if he managed to blow every shit up on Earth?)
(Source: boxart from local stores posted in Bahamut, which apparently took them from 4Chan)
Edit: got Ninja-ed, but meh.