It really just depends on your personal preference. One isn’t necessarily better than the other. Sit-on-top ones are a great option if you don’t like the idea of being confined and/or are afraid of not being able to get free if you tip over. A lot of kayak fishermen like the sit-on-top ones too. The sit-in ones tend to feel more stable. Plus, their center of gravity is lower, which actually makes them easier to move through the water.