Erm...to me, this is tough.
Count Dooku - Count Dooku is a practitioner of Makashi, possibly the oldest lightsaber form known. Considering how Makashi is a form based on lightsaber-to-lightsaber combat - and the fact that Dooku has around eighty years of experience wielding it, I would say he is the superior duelist.
However. Darth Malak is probably a little more superior to Dooku in the Force. He isn't as efficient or as disciplined as Dooku is and he now lacks the experience when comparing age...so...erm...
This is tough - but I really wanna say Count Dooku wins.
See, this duel brings in a lot of hidden variables. Most people would say Malak would win, because of his superior skill and experience. That is because Malak is the duelist of a much older generation. But Dooku is at least twenty-five years older than Malak (maybe more) and practices a form of dueling that was around in Malak's time.
Malak was powerful, as him being able to operate the Star Forge has shown. He may have the slight advantage in the Force. And Dooku is no where near leagues above him. But Malak reminds me of Anakin to a degree. He is rash and headstrong. Dooku is neither.
Malak might win this if he kept his head and his resolve. Because other than that, they are about even. But intellect and posture in battle means a great deal - so I think Dooku wins. But far from easily.
Dooku is at least twice Malak's age, no doubt. Malak is in his thirties or so during his peak in KOTOR.
However, it is the experience here that counts. And not experience in training, sparring, etc. I mean battle, war. Now Dooku, being a Jedi, obviously went on missions both diplomatic and requiring aggressive negotiations. But Malak, he fought through years of straight war as a frontline general. Other than the occasional duel, which was more than enough to keep him in tip-top form, Dooku saw little battle. Now, his eighty-three years may nigh nullify this advantage born from constant battling, but it won't nullify the hard-won battle-savvy and tactical precision brought by war. I'd give them both a high, very high, dueling skill. As to who is superior, I cannot truly say.
As for other factors:
Force Power
I'd have to give this to Malak, but by a close margin. He simply has a larger reservoir of knowledge present at his day and age.
Miscellaneous
Malak has, easily, the advantage in size and brute power, being three inches taller than Dooku, and obviously, his rhinocerous' strength. He'd also have better reach, along with fast and powerful swings. He could keep Dooku from using the most of his Makashi finesse with his four-foot blade as well; he could probably have a swing radius of seven feet.
And Malak being cocky? He's shrewed in his own right. Cowardly? He's never run from a battle in his life. Hot-headed? He's as controlled as you can be, although I'd give Dooku whatever advantage a lack of this would present.
Overall? I'd give it to Malak. Combine swordsmanship to die for with Force powers that have been the bane of many, and a physique that'd put a Gamorrean to shame, he's got some good advantages, although Dooku would present what would be, arguably, his greatest challenge yet.
Well...
I think Dooku will take Malak.
Talking about experience Dooku has a great advantage here. Fighting as a frontline general will give you some experience how to survive on a battlefield but where should the "duelling skill" come from ? There won't be many duels to fight in a full scale war if it's X Sith / Dark Jedi + normal soldiers vs X Mandalorians or normal soldiers + Jedi.
And Dooku was trained for lightsaber duels only. He uses the best duel form he practiced against people like Yoda and Mace. He stayed alive versus Yoda and he toyed around with Obi-Wan and Anakin at once.
For force powers: This is speculation. We know that Dooku had a great potential being one of the most powerful Jedi the order had in the last centuries. Then he had - at least - 7 decades of training as a Jedi (two or three times of what Malak had) and 13 years of Sith training (again twice as much as Malak had). And Malak is not learning as fast as Revan.
Malaks physical advantages are nice but not even worth mentioning when it comes to a lightsaber duel. Revan did defeat him and Revan was (as far as it can be seen) smaller than Dooku and physically weaker - that really doesn't mean much.
joey actually has a good point if the duel is in the starforge malak would win not easily but he would. ouside of the forge though i'd say dooku. if you've read labrynth of evil at one point dooku getss all upset about grevious and his IG-100 magna gaurds practicing fighting. it's not about strength in lightsaber duels. yes it can help but compared to a dueling perfectionist they can parry the blade easily. so i say dooku takes it but it won't be easy for him.