Each of these types has their pros and cons. A sit inside style is great for things like rivers and white water. These will allow you to also go in high surf conditions without getting wet (with an addition of a spray guard). Most of these kayaks have some dry storage for your sensitive electronics or extra gear. They may not have a bungee system which can leave them lacking in the storage department. This style is also ideal for beginners as they allow you to have a lower center of gravity and therefore a more stable ride.
A sit on top type fishing kayak will have a more open deck. In fact, your legs will be completely exposed. This can give you more open storage in the way of bungees and deck space. But it may lack dry storage like hatches.