both have armor no prep time
I'd say Shephard takes this. I've only really played the first game of each series, but Issac felt weaker and more vunerable than Shephard (he is just an engineer, not a Super Soldier). And I'm pretty sure that Shephard has more ammunition in his or her gun (thousands of shots from a slab of metal if I remember right, whereas Issac had only a few, due to the survival horror nature of the game).
So I'd say Shephard takes this.
Shepard has better technique on top of much more combat experience. You can see it in their melee attacks. Shepard's has a refined look to it. Isaac swings like a barbarian. Not to mention Shepard has regenerating shields while Isaac does not, unless he gets some in Dead Space 3.
Shepard takes the win easily.