If I came across Vader, I would probably faint, Jedi training or no Jedi training.
I agree with Jonax that one of the main reasons was probably the terror Vader evoked in his opponents: for one, his physical appearance alone (his inhuman look, his mechanical, "cold" breathing), as well as his aura (his strength in the Force, the amount of darkness he carried with him).
I've read fanfictions about Order 66 survivors encountering Vader and those described his presence as "freezing", that his presence alone would lower the temperature of the location they were at, which is pretty much what I would imagine his presence felt like. So, Vader definitely had the psychological advantage on his side.
But of course, Vader was also strong in the Force (even after his "incident" on Mustafar) and a great fighter, so, his skills were probably anyway superior to most Jedi
(Edit: I just realized you meant during Order 66, not some time after, so his suit-appearance shouldn't be considered)