Honestly, I believe that Kimimaro and Lee are both equally gifted in their
natural movements, though when delved into more specifically, they are gifted in different categories of "speed". When broken down, "speed" is separated into two different branches: linear speed (time it takes one to run as fast as possible in a straight line from point A to B) and multi-directional speed (how quickly one can accelerate, decelerate, and accelerate again. In other words, how efficient one is at stopping/cutting, changing direction, and getting back into their sprint again). Of course "linear speed" is widely accepted as the definition for "speed", and multi-linear is known for the other term "agility". In this way if Lee and Kimi were to compete against each other in a straight-away race, I would bet my money (hands down) on Lee since he has the faster speed. If the competition was to see who can dodge a volley of kunai/multi-directional attack the longest and remain unscathed, I would say Kimimaro since he has the faster agility. Trying to say which of the two is "faster" is like asking which one is taster, an orange or a tangerine? It's all circumstantial.
I based my conclusion on Kimi having a faster agility (just for the doubters) on their match once Lee went into drunken fist mode. It was only until Lee was in DF mode (aka after they sparred at their "natural" un-enhanced level) that he was able to land one hit on Kimi. Of course, by using DF, Lee's movements had become incredibly hard to read. By making his movements hard to predict and read, this is the same as having each one of his attacks taking Kimi by surprise. Even Mei says it:
If an opponent manages to get behind you and attempts to stabs a kunai into your back at near point-blank range, is it logically possible to dodge the attack unscathed? >.>
Though perhaps not with a kunai and not necessarily from behind, this is basically how Lee's attacks were "unpredictable" to Kimi. However, despite being caught by surprise with each "point-blank" move (this is still while Kimi was un-enhanced), Kimi was able to keep up and only have one blow land on him after evading/parrying the rest. The only time Kimi used his curse seal on Lee was to match the "unpredictability" of the DF with the "unpredictability" of his bones
[here]...which pretty much shut down the DF. Defeat unpredictability with...unpredictability haha. On one hand, while Kimi was able to handle his own against Lee's unpredictability, when Lee himself had to fight a very similar tactic, he had his ass handed to him. Once DF failed, Lee unlocks the first gate which is immediately shut down without even a blink when Kimi uses his ability to bone manipulate. This shows that the speed at which Kimi can utilize his bones is
at least the same as a person using the first gate and Omote Renge.
Also, I just had to throw this out there, but the argument that Lee has his weights on is not a substancial point (in my mind) since there is no mention of him wearing them. Having just come out of the hospital with the knowledge that he cannot push himself to hard, it would not make sense for him to wear his weights that are designed to handicap him...when Lee knows full well that he is already handicapped. Because of this, I actually believe that he is not wearing weights during his battle with kimi. Despite not having weights in the beginning, Lee is still unable to land a hit on the Kaguya until he used an enhanced technique. Though just as it can't be proven that he was wearing weights, it can't be proven that he isn't...so the debate regarding his weights can't be used as significant evidence for either side xD.
TL;DRTrying to say which of the two is "faster" is like asking which one is taster, an orange or a tangerine? It's all circumstantial. Kimi has faster agility while Lee has a faster straight away speed.