I would still say Tsunade does.
1. Experience: Tsunade's combat experience and career as a shinobi FAR outclasses Neji's. Additionally, growing up in Konoha would make her knowledgeable of the Hyuga style, and have thought of ways to combat it. Just look at Kakuzu vs Kakashi and Team 10. His experience resulted in Kakashi on the ground twice, and twice in positions where he was dead if not for outside help saving him. Experience always plays a significant factor in fights.
2. Strength: In terms of physical strength, Tsunade has one of the highest physical strengths in the series. Even without enhancing her strikes she can crush walls and the earth. So even if her points end up being blocked, she can still dish out the physical damage to hurt Neji if he decides to try and block a punch.
3. Ninjutsu: While in a later phase of the fight making it useless...due to the gentle fist... the early stages can call for her to utilize techniques like the one she used on Kabuto where she re-wired the nervous system to make different body parts move different things. Had she been going for a kill, Kabuto would have been done at that short interval from when he was unable to figure it out.
It is also important to keep in mind that Tsunade is not a pushover when it comes to hand to hand combat. Sure she doesn't have the most elegant style, but if it gets up close, one grapple or one punch that should have been dodged instead of blocked is most likely game over.
Even more so, Tsunade can keep her distance and use the power of her strikes to disrupt and effect the ground around Neji.
I'm glad you respect and understand the power of the Gentle fist; however, between her combat strength and her own natural physical strength without enhancements... I don't see Neji winning. The fact we eliminated a summon for Tsunade should be enough to show that she is stronger.
