Not much difference really. Ball lock are a little taller and skinnier, pin lock are a little shorter and fatter, if that matters for your future size limitations. Ball locks are more expensive these days (~$40), where pin locks can be found for cheaper ($25-30). If you buy MFL quick disconnects for your tubes, you can switch pretty easy between the two different types if you want to have both around. I think most people started off with ball lock because there were more available, but then demand and price went up. As far as I know there's really nothing better between the two as far as compatibility (ball lock parts might be easier to find locally, but with the internet pin lock won't be difficult either).
Also it is impossible to accidentally hook the gas pin lock QD up to the liquid pin lock post and vice versa. With ball lock if you don't pay attention you can force them onto the wrong posts and wind up getting them stuck on there, but the QDs are color-coded and I've never had the problem checking before attaching. I guess to remove the pin lock posts you also need a special adapter whereas with the ball lock you can just go out and buy a hex wrench.
Really I'd just go with whichever is most available to you now, and buy MFL QDs so you can add an additional type if you desire in the future.
