Well heres the thing, in terms of physical strength, Lee has the flat out upper hand.
If you took away Nejis chakra control and made them have a taijutsu fight, Lee would win, he has speed, top notch taijutsu and insane strength, and thats all before opening the gates.
In a fight however, not limited to one small section of their skills, theres much more to be said.
Its interesting how everyone just up and says oh Lee has the gates, he would win! Gates take time and consentration to open, Lee doesnt just blink them on, he stands there vonerable for several moments as he opens them. that makes a MAJOR open point. the reason why Gaara never finished him then is because he was stunned from the secondary lotus and was unsure of what Lee was doing.
Neji is much smarter than that, seeing his chakra building insanely he would rush up while he was vonerable and seal his points thusly causing a buildup in Lee that would severly damage him and end the fight.
Lee would need alot of timeing and luck to pull the gates agenst Neji, remember they were sparring partners for years, Lee never beat Neji then. The gates being his trump card was removed during the chunin exams sence he revealed it infront of everyone.
If Neji somehow didnt know about Lees gate abilities THEN the gates would probubly deside the match.
In a plot upheld fight between the two of them, Neji would most likely win unless Lee figured the best timeing to use the gates.
Neji still has his spinning defence if Lee were to get that far with his gates either way. Gates can only be used for a short time, Neji would be aware of that fact and just defend untill Lee gave out.
And all of this is after completely disreguarding Lees injuries have not 100% healed, yes hes back in action but hes not off just yet.
