Depends on what you want to do... I like my sit on top for fishing, i also like it because if water gets in, it just drains from the scupper holes. It is pretty much unsinkable (unless you bust a hole into the hull) so for me, it seemed the most practical and safest. You can also stand up on some Sit on tops and use it like a paddle board if it is wide enough and you have good balance.
I never used a sit in kayak, so, i can't really say much about them, i'm sure they have their pros too, but again, it depends on what you want to do with your kayak and what kind of water you'll be using it for.