Among the Decepticons, finding a genuinely loyal and competent second-in-command is a near impossibility. Cyclonus is the exception to that rule. Created by Unicron, Cyclonus is a being whose loyalty to Galvatron and the Decepticon cause is so intense as to exclude most other emotions and interests from his mind. He is dedicated to destruction in his leader's name.
He also has brains to back up that dedication, power to enforce Galvatron's will, and the initiative to form plans and get them done. Cyclonus could easily rule the Decepticons himself if he so desired, either as a power behind the throne or directly overthrowing his psychotic master.