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I wish most new evil teams were more like Team Rocket, dangerous mafiosos moved by simple greed and such. It seems that now we either get the grandiose ultra ideological world changing groups with "good" intentions but retarded execution, like Team Magma/Aqua, Galactic, Plasma, and Flare, or the the complete other end of the spectrum and have them be just dumb, barely threatening ruffians like Team Skill or, even worse, Team Yell (which I didn't even remember the name of or that where even considered the "evil" team for their games).
I wish that plots were more small scale and personal instead of all these grandiose save dah world storylines we've been getting since Gen 3.
I wish the legendaries were something you go out of the way to find, and that their lore was something you mostly got from exploring the world, instead of them being shoehorned and forcefully battled/caught in the main quest.
While I appreciate that they removed the need for wasting move slots with HMs, I hate how they executed it. By simply using rental Pokemon, it completely removes any feel of "adventuring" that these games still managed to have (which has been decreasing with each recent installment). They could have had obstacles that you need Pokemon with certain attributes to get through, just not taking move slots. Like having a big water Pokemon that you can ride, a big flying one to fly, a strong one to move rocks, etc, without having to take an actual move slot.
I absolutely despise forced exp. share, affection bullshit mechanics, and how easy and handholding the games have become. They were already easy games since Gen 1, there was no need to dumb them down even more in the recent installments.