I see this as a narrow victory for Kakashi. He definitely has the edge in ninjutsu, with counters to all of Itachi's elemental techniques. He has also shown more variety and versatility in their application.
They are roughly equal in taijutsu. Itachi has an advantage in speed, but not a large one, and it's hard to say how much of it is from the Sharingan. Kakashi has the advantage in strength, with the First Gate, (not counting any possible other ones) and another slight advantage in stamina. It's hard to say how much Itachi was hindered by his disease, but it was likely significant. However, without the Sharingan draining his chakra, Kakashi has, to my mind, slightly more stamina than even a healthy Itachi.
Genjutsu clearly goes to Itachi. He has more demonstrated techniques of a higher potency than Kakashi. On the other hand, it's not clear how much of the genjutsu expertise is due to the Sharingan. I can only recall one example of a non-Sharingan genjutsu cast by Itachi, and that was channeled through the Akatsuki ring, which likely had special features incorporated. Without the Sharingan, I place Itachi on roughly the same level in genjutsu as Kurenai, given that he was trapped by her and had to use the Sharingan to reverse her technique.
Intelligence-wise, I figure that Kakashi is the victor. For one thing, he advanced earlier thorugh the Shinobi ranks. Yes, there was a war on, and there was a lack of manpower, but that holds true in Itachi's situation as well. The village had suffered through the Kyuubi attack, with a decent chunk of their forces taken out, as well as the loss of three legendary ninja from the Konoha-area forces (Minato, Jiraiya, Orochimaru). But that isn't the point.
In their first confrontation, Kakashi appears to have the situation in hand until he's trapped in the Tsukuyomi, a genjutsu of unheard-of potency, cast by the totally unknown (to him and most of the Shinobi world) Mangekyou Sharingan, and loses. This doesn't really count in Itachi's favor, in the intelligence-stakes. Random, unheard of powerups do not mean you have outwitted your opponent.
In the second fight, while Itachi doesn't have more than 30% of his chakra, he's also legitimately outsmarted. Both parties now know roughly what the other is capable of, yet Kakashi traps him in a deadlock by having him genjutsu a bunshin. (and having Naruto Rasengan the crap out of a corpse, but hey).
So, first fight goes to Itachi, via him revealing one of his trump cards, a pretty much impossible technique. (Cast with the Sharingan, which is banned this battle.)
Second fight to Kakashi via fooling the opponent with a bunshin.
Kakashi is smarter.
Also, nin-dogs are cooler than ravens.