I vote for Samus to win, even though in a battle, I think Ventress would be more likely to. Sure the armor might hold up to a couple glancing blows, like that of Darth Vader, but a well trained Sith, who deflects laser blasts all the time won't be too out of her element vs. a power beam.

Maybe the Morph Ball Bombs and Power Bombs will have an effect, but I wouldn't count on it with force lightning and force push to keep Samus from getting close as a morph ball, and punishing her if she does. Missiles might be less useful.

I just like Samus as a character better than Ventress, so, call it personal bias.