I have a sit in. I see the benefits to the sit-on-top styles from a pure fishing perspective. You can stand and cast from them and being a little higher up helps with some lure presentations.

I use my kayak also for camping out of. I think a sit in offers you a little better boat for that task.

You might try one of the native watercraft "hybrid" (my word) style boats. It is some kind of love child of a canoe, sit in and sit on top kayak. They look pretty darn versatile to me. Though expensive.

These guys aren't the big name that Jackson or or some of the other outfits are but they make a nice boat (and a really nice cooler too.) > http://vibekayaks.com/collections/kayaks Based out of Georgia I believe.