Neji wins. We've seen that lee no longer has an advantage over anyone with his base speed, and if lee goes gates, neji has intel on the effects of gates, so all he would have to do is play on the defensive, which is what neji's kaiten is perfect for.
This is been made several times and Lee wins.
Lee doesn't win until the day he actually tries fighting Neji again so don't state it like its a fact.
Lee only knows close-combat which is what neji´s gentle fist is for, if he closes his chakra points then when lee tries the gates(chakra limiters), the chakra won´t flow to certain places and will do way more damage then when he normally use them and when that happens, neji wins simply.
However, the one thing lee got going for him is his speed when he takes off his weights and he can use that to push neji to his limit while staying out of his gentle fist and then use the gates which will mean the end for neji.
Im gonna say Neji. If Neji has always beaten Lee before the timeskip, Im sure Neji and Lee have both gotten stronger, but the same power gap remain. Gentle fist mixed with bykugan makes the best taijutsu. Lee opens gates? Neji uses rotation. Lee tries close combat? Neji has gentle fists, or completely cut his chakra circulation. Lee takes off the weights? Neji's byakugan can follow his speed, and his rotation will stop from landing his hits. Neji can make his rotation as strong as he wants in according to the opponents attack. Neji wins, also neji has ninjutsu in his arsenal as well, so if lee does manage, substitution, or clone can be added into the mix.