Are you talking about a new boat or a used boat? And are you comparing a 16" with the 13.5" If new, I assume they still have the 15' sport. I have an older (85) 13 sport. I can't say i have tried a carolina skiff, but I see a number of them. I know the 13 whaler is a small but stable boat. On a nice day I go out into the bay - otherwise I stay back in the patuxent river. It is cramped with me, my two kids, and rods. Depending on the use, I might be tempted to go for the extra room if the money was the same. But my whaler is solid and stead (kids can stand on the edges and it stays stable). Just my thoughts.
Couldn't help but add one more thing - the forum on http://continuouswave.com/whaler/ is an amazing resource for whaler information (forum link is down the page on that link). Post your question there and I am certain you will get excellent answers.