I would go with the longer barrel. Usually, they have better accuracy and a touch more velocity. But it really depends on how you are going to use it, small could be better for you. My G3C is much more accurate with the longer barrel. (4" custom fit barrel) Both versions have had great reviews-it's really up to you.
Well, any good member should tell you to get both!
That being said, I'd probably go with the smaller of the two, as I see that as more versatile (easier to store, easier to conceal, etc.). Take it for what it is worth, however, I'm not in the market for either.
As already said, it's whether you're looking for a more compact gun to carry, or a bigger gun to maybe pull home defense duty. You'll always get more velocity from a longer barrel, but sometimes that's prohibitive for what you're looking to do with the gun.