This a common point brought up often, but one I find doesn't hold up in practice. I have both, and except for a little protection from the wind, I get wet from paddle drip in both. You can put a skirt on the sit in, but that won't protect you from hypothermia if you get dunked, so a dry suit or waders and a dry top are pretty much mandatory when the water turns cold.
The sit ins are cheaper, lighter, and in some circumstances easier to get out of, plus most are a little more maneuverable.
The sit on tops are virtually unsinkable, have more room to carry stuff and it can be reached, something not possible in a SIT. They are however heavier and more expensive in comparison.
Anything worth fishing out of should have a lot of secondary stability.