Meh. All of the evil organizations (save Cipher, which technically isn't considered part of the main series anyway) have outfits that directly correlate with their name and/or their purpose.
Team Rocket is dressed in mostly black with a simple 'R' to emphasize that they're thugs who are just out for money in power (exceptions being the Executives, but you could argue that they're the 'white collar' criminals).
Team Aqua has a pirate theme going on because they want to expand the seas while Team Magma has a volcano theme because they want to use Groudon to create more land.
Team Galactic's members all looked like weird futuristic space people because Cyrus seeks out the Pokemon that control time, space, and antimatter.
1st incarnation of Team Plasma resembled knights. Presumably, this was to symbolize N's innocent outlook in wanting to save the Pokemon (the gallant knight saves the day). Their second incarnation, in which their front of benevolence has been shattered, is more obviously shady.
So while not all the uniforms are aesthetically pleasing, they serve their purpose.
Team Flare has the flame suit going on and right now we can only guess at their goals. How cool would it be if they turned out to be like the Men in Black? Except you know....orange/red and not the good guys...