Unlike cookie-cutter villains, they believe what they're doing is correct and for the greater good as Rezo (Ghetsis) is leading them to believe.
That actually describes a lot of villains.
To put it in perspective, Dungeons & Dragons actually describes antagonists pretty well by filing them into specific categories. These are:
Chaotic Good: The people who honestly believe that what they're doing is
right, but they don't see that it's most certainly not. They act on this mistaken ideal by resorting to destruction or anarchy in order to make room for something new and better. (Yes, I realize that chaotic good also describes
protagonists who just don't give a crap about rules. Panty and Stocking in
Panty & Stocking with Garterbelt are a perfect example of this side.) As an example, let me tell you about a couple of other groups. There's a couple of groups who work to make the world more habitable for every living thing in it. Then, there's another group who want to create a brand-new world (not necessarily scrapping the old one, even) in which they can set up a utopia full of peace and order.
Incidentally, who are those organizations? Well, the first two are
Teams Aqua and Magma. The second?
Team Galactic. All three (in the games anyway) felt that what they were doing was absolutely right and necessary. They just did incredibly dumb things to get their goals accomplished. (And at least Teams Aqua and Magma realized how moronic those methods were. Cyrus just went off his rocker instead.)
Lawful Evil: You ever have an evil government that happened to be elected or born into the office by completely legitimate means? You know, the kind that oppress the people using the laws that they have every right to create and enforce? That would be lawful evil. Or the entire premise of
1984.
Neutral Evil: The kind of evil that's not necessarily psychotic (in the incoherent, mass-murdering kind of way) but the kind that doesn't really color inside the lines, if you get what I'm saying. They're the kinds of villains who just don't care about
your rules so long as they get to play by their
own. A lot of what people would think of as stereotypical villains would probably fall under this category for the simple reason that a lot of villains are after world domination/setting up a new world order/whatever just for the sake of being evil, rather than because they can back up their evil with good ideas on one level or another.
Chaotic Evil: The Joker.
But seriously, chaotic evil attempts to overthrow the government, sets fire to orphanages, and jaywalks. Why? Because it's
fun. These are the characters who are out to destroy order, the world, as many buildings full of innocent people as possible, not because they want to establish something instead or because they want power but instead because they can.
In short, what you're describing is actually a classic example of chaotic good. There's a lot of examples of this, especially in Pokémon canon. That isn't to say that it can't be new and original. I'm just saying it doesn't necessarily prove otherwise. That's why you'll need to work hard at making sure everything
else about your characters doesn't sound cookie-cutter.
Al is meant to be the brother of one of the main characters and a drama plays out between him and his sibling. It's to be a defining point in the series. Of course, I can't spoil it.
As I've said to you via PM, this kind of thing is pretty much
older than dirt. In fact, I'm planning on using the same idea myself, only the characters in question are father and son, not brother and brother. Again, it's not necessarily something that will automatically be labeled as unoriginal if you do it, and it's still possible to be pulled off. It's just that this idea is more of a trope, so it won't necessarily convince people either way.