Okay I am going to say this. Not because I am a Shikamaru fan but think about it. First of all, When you think about both the Anime and the Manga. Yeah Neji is powerfull and he is Clever to boot. First of all take all the things that Shikamaru could do. They might be little things but combined with his Genius Intelect it could be dangerous. First of all He has his Typical genin Moves that could become handy. Replacement Techniques, Bushin No Jutsu. He has good accuracy not as accurate as Ten Ten but still Good enough. His Shadow Imitations are not limited to just Binding Or Better known as Kage Mane no Jutsu. . He has the Shadow Neck Bind which breaks somebodys neck/Kage kubi shibari no jutsu. . Though unless you have powerfull Chakra like Naruto or something like that. Then there is his other technique of shikamarus which is the Kage Nui or Shadow sewing in which his Shadow of course turns into many tendrils adn then they can come out of the ground whip and Piercing Objects. So that along would give him some plot Ideas. Though also take in to Consideration that Neji knows Shiikamarus a Genious but then again Shikamaru knows that he knows and will plot against that. Then again... Neji would probrably win because shikamaru would think it to troublesome and just give the fight up to Neji.

I tink too Shikamaru would just give up because its too troublesome and he doesnt even need to fight Neji

Bear with me. This will be a long post:

Episode starts, theme song, etc.

Neji begins by activating his byakugan, Shikamaru begins by using his shadow imitation technique. Neji quickly dodges it, while Shikamaru throws several kunai. Neji blocks it with Hyuuga heavenly spin.
Shikamaru grins while saying something rebellious like "Too bad that can't block shadows!" Sending his shadow under the spin. immobilizing Neji.
Neji shoots Chakra out of his entire body dispelling the shadow imitation technique.
"You should have realized that I would see through your technique. You have a specialized chakra that's nearly paper thin, and to disguise it you hide it in your own shadow! Even if you immobilize me I can still use my gentle fist to destroy it!"
Neji rushes at Shikamaru attacking his tenketsu. Afterward neji triumphantly says "There's no way you can beat me, you can't even use chakra anymore." Shikamaru chuckles as the Kunai he threw earlier explode (from exploding tags wrapped around them) launching dust into the air. Neji take this as an attempt to block his vision (which it, of course, doesn't) but finds himself unable to move.
"W- When did you use shadow imitation technique?" Neji stutters
"I can flow my chakra through ANY shadow. Dust is simply small particles suspended in the air. All I had to do was connect the shadows on the small particles to reach you. I was able to extrapolate where my other tenketsu were after you hit the first 5. If you know where they are, it's easy to make your opponent miss such a miniscule target."
Neji Laughs saying "Fool, I'll just break your connection again!" Suddenly arms of shadows wrap around neji's head forcing him to stare into the sky
"Without those eyes of yours you won't be able to properly regulate you chakra. The byakudon doesn't just allow for you to see other people chakra, you can see your own too, and without its help you can't regulate you chakra well enough to emit chakra throughout you entire body!"

Ending: Shikamaru gets tired and quits, while neji confidently says "I would have beat you, you had no chakra left" Then Neji finds an inactivated exploding tag hidden in the ground, left by Shikamaru. Neji looks at Shikamaru solemnly as he walks away.

Official Winner: Neji
Unofficial Winner: Shikamaru.

Basically, in every Naruto episode, the underdog always wins (Unless your fighting Sasuke), meaning Shikamaru would win.

masaaki, is all that about shadow bein a thin piece of chakra and how u need byakugan to regulate chakra tru? or did u make it all up? and if it is tru wher did u find out this info?

I just kind of made it up... It seemed like it would work. In the Manga they've mentioned vagueley that for moves excusive to clans they use different types of chakra. (somewhere between 315 and 325, when Kakashi is teaching Naruto about elemental moves) So I just guessed.

meh, i think Neji would win.

Masaaki´s story has a flaw: when Shika forces Neji to look into the sky Byakugan will still be able to see the chakra, because it has a 359º field of vision. Also, Neji doesn´t require it to emit chakra through his body...Anyway, cool stroy, this fight will be very cool with Shika trying a lot of cool strategies to trap Neji and Neji using different techniques to evade them...In the end, I think it will be Shika the unofficial winner and Neji the official winner, both chars are great and very popular and Kisi won´t make one look worse than the other