Could go either way. In base they are roughly equal. Bee has an outstanding style when Kakashi has Sharingan precognition, plus superior ninjutsu(i believe they are around the same speed though). Kakashi has shown to be much more clever than Bee in a fight. His Raiton Kage Bunshin could paralyse Bee, adding his other ninjutsus and Bee would be quickly screwed if he continues to fight in this mode.
Bee enters V1 or 2, and we've seen Kakashi able to react against multiple V2 just fine(V2 who were causing a lot of problems to Bee and Naruto btw), so he could react to Bee in these form without problems, counter/dodge if needed. If Bee enters his full version Hachibi, he can use the whirling, but to use it takes some time and we have seen Tobi able to escape in time by jumping over a tree. Kakashi on the other side has a perfect technique to avoid it(doton hiding mole). If Hachibi uses TBB, Kakashi can kamui it.
So like you can see, Kakashi has shown enough feats that prove he can counter almost all Bee moves. On the other hand, if he stays in Hachibi mode, he becomes an easy target to get kamui'd and again we got a proof that Kakashi is able to kamui him even in this form.
Wow, i actually thought it could go either way, but now i think that Kakashi has more chances to win