While I feel that the topics addressed by the inclusion of Plasma and Bianca's Father were clever, I have to say that the main lie of Pokemon games wasn't the place to put these.
Plasma's conviction was warranted, but regardless you had to stop N and Team Plasma with no thought paid to of how you felt about the subject because that is what the story demanded.
Because Pokemon is... Well, Pokemon, it's obvious that the player was going to be against the ideals of N and Plasma regardless of whether it was justifiable or not.
I won't go into whether I agree battling is right or not... But aren't Pokemon Rangers proof that there's a way of living with Pokemon without using them to fight?
As with Bianca's Father... This topic was handled poorly. Terribly so. There is no way a child of Bianca's age would be out on her own, Pokemon or not(as a matter of fact, animals with dangerous powers would ADD to why she wouldn't be alone at her age).
What GameFreak tried to do was address topics that would affect Pokemon if it was set in the real world and because of that, it suffered. There are lots of questionable goings on in Pokemon, but it's a world that shouldn't be taken so seriously in regards to some topics. Not when you're a kid whose end-goal is always going to be defeat the champion and catch them all. I'd rather actually interact with real people about these topics, rather than read speeches that I'm going to have to unconditionally agree with.