To begin with, cut the funky-dunky hand-dandy gadgets that Bond has. Let’s look at their minds, their methods. Bond is swarthy, and tough… a “man’s man”. He relies on his fists and his gun as often as his intellect. Additionally, he does something that Holmes would never do: He relies on gut instinct, and luck. He takes crazy chances, and allows his passions to get in the way of his rationality. But he gets the job done.
Holmes, on the other hand, is a walking brain. He leaves nothing to chance, or to guesses, or to instinct. He observes everything, and always makes sure he has a way out. He doesn’t allow anything to cloud his logic. However, his brute-force factor is decidedly low, and if he gets outsmarted (rarely, but it happens), that’s when he gets in a bind.
So who’s the better agent? Who’s better at solving the case? Let’s forget the case matter for a second (i.e.- “Bond is better because he’s saved the word dozens of times”) and just look at who’s better at doing what they set out to do. Who’s got the better methods? Who’s better at figuring out his situation? And who’s got a better drink?