My problem more than anything is that Lysandre's motive and Team Flare's Modus Operandi don't really have any discernable correlation. Team Flare just seems like they're generic show-offs concerned with image, attention, etc. Lysandre has a more nihilist "the world is doomed with humans" outlook and thus set about effectively trying to cull the population.
I don't see how these schools of thought correlate to even make some kind of weird warped version for the grunts. With Jessie/James/Meowth in the anime, they're certainly goofier than most of the other TR villains, certainly than Giovanni when he gets involved, but they have the same basic goal in mind: steal Pokemon and use them so Team Rocket can take over the world. It just happens that the main trio is played for laughs because they're a recurring threat and we're used to dealing with them, similar to random team grunts in the games. Lysandre feels like a sloppy twist because his motivation doesn't match how his team acts even in an abstract manner, and unlike someone like Ghetsis, that contrast isn't played as a betrayal.
To borrow from Plasma and grant some leniency with the repetition of this scenario, a better "swerve" with Lysandre would be if his team was some kind of Plasma style human or Pokemon extremist group. The grunts engage in the misdemeanors we deal with throughout the game, sabotaging reserves, "catch and release" from things like the daycare, etc., but Lysandre takes a more extreme solution than N's extreme-but-honorable approach of attaining power. Lysandre decides that Humans/Pokemon can never live well with the other, so he implements the plan to wipe out said other. Still extreme enough to stop them, and there's a connect in motive even if not in threat level or mood.