Ghetsis, I have to say is my least favorite character in B/W, and one of the biggest flaws in the plot too, in my opinion.
He completely ruins Team Plasma's entire motivation for doing what they were doing. It's arguable that there probably were people in their ranks that legitimately felt that way about Pokemon Training (though using Pokemon Battles to make their point is rather hypocritical if you ask me, but I digress). And the messed up thing is, I actually found those motivations and goals far more interesting than Ghetsis' motive of basically wanting to take over the world by being the only human with Pokemon. When I defeated a Grunt and they said things like, 'Are you happy knowing that you hurt Pokemon for your own amusement?', I started questioning it myself. When a villainous group can make the player legitimately feel like they might be doing something wrong, that's how you know you've got well-written antagonists. But Ghetsis ruins all that with his motive.
Not to mention, this is all kind of thrown at you at the last minute with only a few hints throughout the game that he might have ulterior motives. Not only were his true intentions detrimental to the subject matter of the game, but he's not a sympathetic villain at all. He's just a straw man, and beating him really feels like an empty victory because of that.
In all honesty, N should've been the main villain instead, because he was far more sympathetic and actually had a past that gave him a reason to be like he was.