Dimensions are the biggest difference. Also, ball lock kegs typically have a manual PRV in the lid, where you can pull it up and release pressure manually. Pin locks have one built in but you can't make it release manually. To release pressure on those you have to push the poppet. I have both and prefer the ball lock manual PRV but they both work fine. I haven't minded my pin locks one bit. I actually started out with them because I could fit a 5 gallon in my fridge(being shorter and fatter).
One downside to pin locks is they're not made anymore, because Coke has a patent on the post style. So you have to buy used. This is not a big deal for 5 gallon kegs, as there are tons of used pin locks floating around. However, I brew small batches and like the smaller 2.5-3 gallon kegs, and the small pin locks are REALLY hard to find. Hence, why I also own a ball lock now.
Edit, an additional note on the lids. The lid size is the exact same for both keg styles, so if you had a pin lock and wanted to get a lid with the manual PRV there's nothing stopping you from doing that. One of my 3 gallon pin locks has one because the lid it came with actually had no PRV on it(WTF) so I bought a new one with a manual PRV.