The closest thing to a singular villain in the games that I can think of would be Darkrai from PMD2. (Sure, he fights with six lackeys at the end, but he orchestrates most of his evil plans all by himself). Although, in his case he worked because he was responsible for a lot of other Pokémon turning evil (like Primal Dialga). Ultimately, the difficulty in making a singular villain is that you'd want to have villains to fight for the entirety of the game, and if the same villain loses to you multiple times they won't seem very threatening.
One way that can work is by having a singular villain and the team villain together. One example along the lines of this would be Purple Eyes from Pokémon Ranger Guardian Signs, as he is not the leader of the villainous team in that game but he is the most villainous character in the game. A similar villain to him in the main games could keep things fresh while not losing the advantages of the team villain.
Just use existing trainer classes that would be employed by the corporation. Have the only clue be the fact the only other place you see that exact combination of classes is inside the corporation itself.