I have both but prefer a sit in during the cold months, I fish out of a Pungo 140 90% of the time. With the high (9") gunnels you can go into rough water, I've been in 4-5' swells with no problem , a sit in will go anyplace a sit on can go, caution and awareness of the surrounding is always needed whether your in a sit-in or sit-on.
Personally , I feel if you fall off or out of a kayak ,you have no business on one.
Floatation is required , whether it's the factory foam or air bags is a must on a sit in , just in case you capsize, the kayak will stay on the surface and you can hop in and begin pumping.
For a beginner I would say "Sit-on for surf and ocean and either for everything else"