I think that they are both incredibly intelligent, Itachi has just always had more at his disposal, and he has had an infinitely larger amount of drive than Shikamaru, who as we all know is lazy lazy lazy.
Now, a fact is that whenever Shikamaru makes a plan in battle, he always succeeds as far as the goal of the plan was. Tobi complemented Shikamaru on his intelligence, singling him out. And to the whole "Kakashi is as smart as Shikamaru" thing, I'll admit Kakashi is smart, but honestly, Naruto is the one that said that, and I wouldn't trust Naruto's judgements much at all, he's pretty biased in Kakashi's favor. For instance, I doubt anyone would say that Kakashi truly has a better sense of smell than Kiba, even though Naruto said so. So I will stick with my belief that Shikamaru is smarter than Kakashi.
Overall, it's really hard to tell, because of the difference in their power levels. Shikamaru has made a lot out of a little because he is so weak. For him, the only way to battle is with his intelligence, because as a ninja himself he is always the less powerful one. Itachi however has the massive power levels to go with his intelligence, so we haven't seen him fight purely with his intelligence as Shikamaru does. But he's a thinker.
In my opinion, Shikamaru has more tactical intelligence. In battle, he can make the best use of what he has at his disposal, better than Itachi, because that's all he does and the only way he can hope to win. He can create the best strategies overall. However, Itachi is more intelligent philosophically. He thinks about things like feelings and what makes people do things on a psychological level. He has a drive because he has thought these things through and seems to understand what is really important. Shikamaru hasn't thought those things, and hasn't come to those conclusions, which is why he is so lazy. That shows that Itachi is a better "thinker" than Shikamaru, but I believe that Shikamaru is a better "tactician". Thoughts?