The Vile Lysandre

Lysandre certainly takes the cake for being the most evil person in the pokemon world.  Let me elaborate.

As the battle came to a close, Lysandre made note that before we removed the Yveltal batteries, the machine still had enough power to be fired exactly once to destroy the facility.  Lysandre was trying to take us all out with him.  Cue Metroid-Style Escape!

Lysandre killed himself while trying to kill the kids that defeated him.  This is a bit crazy, but the thing is, he kept his pokemon on his person when this happened, so he also killed all of his pokemon.  I can't be the only one that finds this a little macabre: he killed himself and killed his pokemon too.  I don't know what could be more evil than this.  I guess the real-world analogue would be if you set your house on fire and died with all your pets and family.

I guess it makes sense for Pokemon to be able to die--otherwise what is the purpose of Lavender Tower?  I have just never actually witnessed the death of a pokemon.  I was the last one to see that Gyarados alive...then I beat it up...and then it was gone forever.  My character was the last person to see that Gyarados, and the last thing I did to it was Aura Sphere it in its big, stupid face.
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The pokemon gang was apparently doing a lot off screen to help the cause and this only came up at the very end.  After escaping from the facility and watching the whole place get vaporized and sucked back into the earth, we all regrouped amongst the ashes. Tierno (the dancing one) was apparently helping to release all the captured pokemon in a nearby route and Trevor was helping evacuate the town (or something). 

The fact that you were a part of a big Anti-Flare effort actually goes a long way towards bringing you in as a believable main character--and makes the world a lot more alive.  This is much easier to swallow than the idea that you could single-handedly take out all the Rockets.  The whole game is a lot more believable from this standpoint.

I never quite got the idea of purposefully disturbing Groudon or Kyogre--who are literally in the process of tearing the world apart at the time that you hunt them down to battle them.  In this game, you do end up fighting a scary legend, but it kind of happens by accident.  When you end-up catching Yveltal, its really only because the thing was so angry from being asleep for so long that it wanted to hurt you.  You weren't just looking for trouble and a new catch, you were attacked and you sent out your pokemon to defend you.  You only catch Yveltal because if you don't, it would hurt you.

A lot about this game is incredibly well thought-out, especially when compared with previous installments of the game.  This may be the best game since Red version.

Current Squad:

GRENINJA/Froakles/lvl.42
VENUSAUR/Venus/lvl.41
FLAREON/Hotfoot/lvl.42
SCRAFTY/Scrappy/lvl.41
HIPPOWDON*/Leviathan/lvl.43
AERODACTYL/Scarydactyl/lvl.40

On Rotation: Lucario, Gardevoir, Pikachu, Skrelp