Characters like Pain are what I'd call rational villains. Villains who do what they do for reasons more significant than greed or power. Pain did what he did because he wanted to create some sort of peace. In Naruto, it seems as though there are a lot of these kinds of villains.
Irrational villains would be like Kakuzu. He doesn't want anything but money. He's superficial. He doesn't want to create peace or anything, he just wants to get rich.
There are benefits to both kinds of villains.
Rational villains are far more compelling and can actually get you to sympathize with them. And because they're usually seeking out something grand (like world peace), they usually drive the plot a lot more than irrational villains. However, when defeating a rational villain, you can't just beat them up. A rational villain represents a belief or an ideology; in order to really beat this kind of villain, you have to break their beliefs and show that they're wrong. A fight with a rational villain is as symbolic as it is entertaining.
Irrational villains make for great minions. Especially in action stories, they can be used as benchmarks of strength for the main characters. While rational villains can be used to drive homes themes, irrational villains can be used to show a growth in strength and this is vital in any action story. With irrational villains, there's no point in talking to them. You can't tell Kakuzu that money can't buy you happiness. And so irrational villains can't be talked out of doing their plans or as naruto forums say: "Talk no jutsued".
Personally, I think Kishimoto should have had a few more irrational villains and fewer rational ones. Rational villains should be rare but impactful. Rarity for rational villains is a necessity because you don't want the readers to get bored and think, "oh great, another bad guy that just wants world peace." You want the audience to think, "you know, this guy doesn't sound so bad..." I know it sounds counter intuitive to say there should be fewer complex villains, but I truly believe that. By decreasing the amount of rational villains, you make the existing rational villains that much more impactful and unique.
I'd like to hear what you guys think. And please remember to use spoiler tags if you decide to talk about the manga :)