Okay, first of all I have to be honest, I'd much more likely form a Justice League like group to combat the evil teams rather than start an evil team, but in the spirit of the thread: This is the rise of my team, the Order of Aurelius (yes copyrighted in our world for those who know the reference, but that name is free in the Pokemon world.)
I'd set my home base in a region most people would never think to look, the region where Collosseum and XD took place in. First I would recruit Domino, the Team Rocket girl from Mewtwo Returns. Then I would have her steal the Master Ball plans from the wherever (Silph Co. I guess) and destroy their copies, since the Master Ball is still classifed they would have no way to prove they created it. Then I mass produce Master Balls and start increasing my resources that way. This way we would seem to start off as a legitimate corporation and not an evil order.
I'd place two infiltrators in each team from every region. Their job is to keep me informed of everything they are doing and I can decide from there what if any counteraction I need to take. Eventually I would either absorb or eliminate the opposing teams and rule every region (Kanto, Johto, Hoenn, Sinnoh,and Unova).
I really have no clue who my generals would be. I'd probably recruit (brainwash, bribery, what have you) some of the better trainers (Ash, Dawn, May, Brock, Paul, Barry, Gary some of the gym leaders) to be my lieutenants who would be promoted to generals when my originals were promoted to region vices.
Uniforms? What uniforms? I mean seriously nothing is more of a giveaway of your allegiance than uniforms. It's called casual wear people. Wear whatever you want. Same with Pokemon, use whatever you want...except a Feebas or Magikarp, cause let's face it they have no power...unless you can convince me otherwise. Oh, and hair color, totally up to you.
Assuming that there are actually muliple legendaries, I would amass one of each of them for myself. The rest would be distributed to my generals (future regions vices) and major lieutenants (future generals).
After a few years, with people undoubtfully using my produced Master Balls, I will activate the one improvement I have made to the Master Ball. The 'Dark' Generator' which would put those Pokemon under my control, similar to Shadow Pokemon except they are brainwashed not closed off. With the control of all of the extra Pokemon that used to belong to their Trainers, we could take down the people and rule all the regions.