I really enjoyed the plot in this one, and what PETA Team Plasma tried to do was completely different even if it was hypocritical - it made for a much more unique enemy team than Team Rocket just trying to take over existing operations or making money for an attack, Team Aqua wanting to flood the planet, Team Magma wanting to erect a new continent, or Team Galactic just doing whatever their boss told them to. Although Cyrus in Platinum was great, N was even better - GameFreak is hopefully listening to us, and the more supernatural, eerie feel of Team Plasma made it more interesting. I also liked how your reinforcements were the gym leaders. I really have enjoyed seeing them be more than statues that command Pokemon.
I hope that in the future, we get more character development, and that your character has more reason for a journey than "I WANNA B TEH VERY BEST LIEK NO1 EVA WUZ." Like, make them go seek their father, now that they're a decent age to. Give them deeper motivation. Same goes for one's rivals. Do something like... you seek your father, your rival seeks their mother. You end up finding that they eloped and he went crazy, starting the enemy team, which was then targeted by a usurper. Something like that. It'd be a lot more to have conflicts within the enemy team - and more realistic too.
I agree with this too - finding yourself really needs to be a big deal. Our character doesn't even talk because it's supposed to be US, and they're not changing that - but if the supporting cast has such storylines, it makes everything more interesting. Imagine if there were eight of these going on at the same time, featuring rivals, gym leaders, heck, even Nurse Joy. Make more NPCs relevant. Flesh things out.