In that case, because there's not much that could matter, we could offer up completely random choices... like Team Fluffy Bunny, led by a giant Mudkip.
To be serious, though, because you know the details of your world and the situation better than we do and because you can't tell us a lot about your story (such as how the evil leader gathered followers, how they operate, or what kinds of weaknesses they would need to have in order to be taken down by the protagonists) without giving us some massive spoilers, it's best to sit down, open up an online Pokédex (like
Veekun) and find a Pokémon you happen to like. Open up a blank word document and write down every name idea you can think of. Things like that.
Yes, I realize that's not at all what you're looking for, but put it this way. We don't know
anything about your story, and the details we'd need to know to help you (because the villain is a massive role to fill that would require us to know all the dirty details of your fic) would just spoil the entire thing for us. So, think about what you're planning for the fic.
Start off by asking yourself how the villain managed to get followers in the first place. Did they use cleverly placed mass-hypnosis? You'll want a Pokémon that can use Psychic-type moves, then. Do they just seem like the last Pokémon you'd expect to be evil? Look for Pokémon that have a reputation for being good. (For example, Blissey, Gallade, Cresselia, et cetera.) Are they just charismatic? Did other Pokémon just think they were the strongest and could therefore stand up to the forces of the power they're fighting against? Did other Pokémon just think they were the
smartest and could therefore come up with the strategies they'd need to fight back? Gun for Pokémon who have those kinds of reputations because more than likely, Pokémon would think with those stereotypes too.
Once you do that, ask yourself why they want power. Lots of newbie writers like to have characters who thirst for power but never actually figure out what those characters would
do with it. (
Megamind has a great example of what happens when this kind of thing occurs. You know. The part where the title character takes over the city and realizes he didn't plan past that.) Figuring out what that character would want based on what they would
need is a way of doing this. For example, a Water-type might want to flood the world in order to live in the kingdom (s)he has every intention of ruling. (After all, you can't very well be an effective leader on land if you happen to be a Milotic.) Alternatively, maybe they want to enslave certain species and elevate his/her own with the thought that they're superior to every other Pokémon -- and mindslaves are easy to create if you're psychic. Or maybe (s)he wants to build massive tributes to him/herself, which would call for a particularly egotistical Pokémon (i.e., one that's not necessarily known for its intelligence).
Finally, ask yourself how that Pokémon needs to be taken down. Here's the part where I have to voice a concern about your plot ideas. You have Pokémon use swords and other weapons, but Pokémon
themselves are living weapons. Why would a Pokémon feel the need to use a sword when they could just blast an enemy with lightning fired
from their hands? This is why weaponry isn't particularly developed or used that often in canon -- because given the fact that humans are surrounded by monsters that wield godlike mastery over the elements, there's just no need for a gun. (This goes especially for the fact that, well, shooting someone with lightning gets the job done faster than shooting someone with a bullet. And it's easier to cover it up and say it happened by some weird natural freak accident.)
Either way, though, every Pokémon will have its weak points, so you'll want to ask yourself how you want your protagonist to take them down. For example, you can't have an epic battle against a Registeel using a sword for rather obvious reasons that involve why it's called Regi
steel. Likewise, a Numel can't outsmart an Alakazam, considering Alakazam are known for having insanely high IQs (and Numel... aren't). Yes, there's going to be natural differences between one species and another.
Not having them is like saying that a human being is exactly the same in terms of strengths and weaknesses to a garden slug. The fact of the matter is that humans have certain levels of intellect and physical endurance that differ from every other creature on Earth, and the same can be said for Pokémon. One Pokémon's level of intellect and endurance (and other things) is not another's. That's why you
do need to consider species on some level while trying to come up with your characters.
To make this massive post short, the gist of it is:
1. The best people to create characters for a story are the people writing it themselves. They know what they'll need, and they know how their world works. Other people don't and can't, especially after only a few lines of summary. No, this is not an invitation to submit a massive summary. You will spoil your story that way, and we
still won't be able to get enough details to create a character for you.
2. If you want to get a character species and/or the name (s)he'd give his/her own organization, chances are this is a sign you'll want to develop the character itself a bit more. Figure out the hows and whys to what that character is doing, and you'll be able to narrow things down a bit.
As a side note, the height is the
last thing you should be thinking about when creating a character. There's not that many Pokémon that are exactly six feet tall anyway. Even legendaries are usually in the four-or-five-foot range.