The Jedi Civil war lasted only for 2 years and we don't know if Malak did anything besides sit his ass on a ship. Dooku fought... Asajj, Sora, Grievous, Mace, Yoda twice... and probably some more I'm forgetting. All since the start of the clone wars.
Granted, he was the second strongest in the Sith Empire, but this Empire only had 2 years of Sith training, contrary to Dooku's 13 years. Malak is also brash, impulsive and known for charging into battle. This is too close to call and Malak doesn't "pwn" anyone. I'm even inclined to think Dooku takes it more often than not.