His very introduction being the CMoA where he quits Team Snagem, takes their Pokémon Snag system, and then blows up the base itself as he escapes, all while grinning like a maniac. Nothing is more badass than that.
Except for right after that, when he reveals himself to have 2 different evolutions of a Pokémon that there's just one of in most games. Not only does Eevee evolve into Espeon & Umbreon through Friendship, they start out at Level 26, when most Trainers start out with one Pokémon at Level 5.
Cipher's multiple subversions of The Guards Must Be Crazy can be seen as this, forcing the player trainer to stay on his toes the entire campaign. Also doubles as Paranoia Fuel, for obvious reasons.
Villain groups typically only attack as a result of the tripwire mentality. Cipher Peons and R&Ds will detect by sight and sound, and will turn to face you regardless of your vector of approach.
Villain groups typically stick to one type or group of Pokémon. Cipher doesn't.
Kids Grid: a bunch of 'children' that are hard at work in rescuing Shadow Pokémon. One of their bases even got a 'satellite dish' working and eventually overpowering a jamming signal that Cipher had placed. Another manages to recover the data of a wiped disk from Cipher. There is litle wonder that they become the ONBS in the sequel!
Ho-Oh shooting down Evice's copter with Sacred Fire.
Eagun defeating some Cipher goons with his Pikachu.