I have stated in the past: "If Lysandre wanted to remove all of the ignorant people from the world, he certainly did a good job of gathering them all into Team Flare". You can't even compare the anime writing to that - Team Flare would be shamed by Jesse and James's comparative hypercompetence.
I think the problem with Gen 6, from all I've personally seen of it, is that the game is trying to make you invested in TOO MANY PEOPLE. Oak and Elm worked because they were there to throw a pokedex in your face and then never got involved again. More importantly, they pushed Mega Evolution WAY TOO HARD; there are several characters - Lysandre and Sycamore included - that would be infinitely more tolerable if the game wasn't trying to shove their core gimmick down your throat at every turn.
tl;dr: Gen 6 is like the Sonic Heroes of the franchise, writing-wise.
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I think the problem with Gen 6, from all I've personally seen of it, is that the game is trying to make you invested in TOO MANY PEOPLE. Oak and Elm worked because they were there to throw a pokedex in your face and then never got involved again. More importantly, they pushed Mega Evolution WAY TOO HARD; there are several characters - Lysandre and Sycamore included - that would be infinitely more tolerable if the game wasn't trying to shove their core gimmick down your throat at every turn.
tl;dr: Gen 6 is like the Sonic Heroes of the franchise, writing-wise.