Hard decission. Most Cipher members (excepting for few ones) look like Power Rangers, but they have a really impressive quantity of shadow Pokémon (obivously because they started this "trend"). Team Snagem went a little bit further in my opinion, because they designed a machine that could steal the trainer's Pokémon.
And of course, there's another variable. Team Mirror B., which is considered by many the best one, even though they're not a big organization, and it's only conformed by three shady-looking guys.
After noticing everything on the game, I'd happily go with Cipher. It was a huge mess in both games, and I don't care the fact that Mirror B. was astonishing, but I really admire how their cruelty could turn naturally pure living beings into sad, fighting machines with no feelings. It was, without using many words, astounding and at the same time, horrible. It's not your typical Evil Pokémon Organization, no, but it was quite more than that. They turned light into darkness.