Amen. PBR was really a disappointment for me because, even after Orre where they actually had a decent plot and motivations, they decided that straight tournament battles with no depth was better. Sure, the wifi battles were good and some of the tournaments were challenging, but it would have been so easy to add some depth to it.
For me personally, I liked it when the old villains were actually bad. I mean, Team Rocket's motto was "Team Rocket will do anything for money." They killed Marowak and Cubone, and sold them for money. Quick thought; where did that Cubone in the Game Corner (pretty sure this is RYB not GSC) run by Team Rocket come from? They performed genetic experiments to create a killing machine. They are bad. Now we have teams with bigger goals but purer methods. Name something in the games that was blatantly criminal. They don't steal pokemon. Magma/Aqua stole a submarine. Sure, Cyrus tried to destroy the world, but what did the grunts do that was bad? They blew up a lake. While not good, not exactly the personification of evil either. Galactic is a bit of a cult, but that's creepy, not evil.
Cipher was the closest to beating the Rockets; who else held people hostage? And when it comes down to making Shadow Pokemon, I'm pretty sure "closed the door to their hearts" is a PG translation of "we psychologically and physically tortured them until they became void of all emotions except anger" (aka got rid of their positive emotions, metaphorically closing the door to their hearts).
While on plot (and stuck on rant mode), a real way of stopping the "evil" group would be nice. Because as nice as it might sound, if bringing Dialga/Palkia into the world is enough to trigger apocalypse, I don't think knocking them out and making them lose any control they might have had then using them to battle even more saves it. Also, that is not something your average 10-year old can do.