Well, Chouji mostly fights up close, which a bit of a disadvantage, for him since Neji specialises in close range combat. If Neji can plug up his points before he transforms, then he could end the match there, but Chouji would likely start out in the butterfly mode.
In that case, Neji would have to use vacuum palm, to really damage him from long range. Because he is so massive in this form, even techniques like rotation would hardly defend him from his punches, though he wouldn't likely need it as He could just evade the blows. He is a considerably fast shinobi who trains under the tutelage of the fastest people in konoha.
In Chouji's butterfly form, he could end the match with one decent blow, but he first has to catch Neji. He could also use the meattank technique to squash him, though it would be easy to dodge as he moves inone direction when using this technique. In all honesty, Neji could just outlast Chouji in his butterfly form, or even land a few fatal blows to his heart with the vacuum palm. He is definitely fast enough to dodge choujis blows and is very accurate with his use of the byakugan.
Choji has beaten Hizachi who was near Hiashis level, who is himself stronger than Neji. How could Choji lose?
He also happened to be fighting Hiashi Hyuuga at the same time who is equal with him in terms of skill.