I have both. The RT is good for long trips, I've done a 1500 mile Iron Butt run on it. I can do strings of 600-700 mile days on it. The S is almost a naked bike. The wind on it can get a bit tiring after 7-8 hours, especially where it is pulling your knees out away from the tank.
The S is really good for hot weather as you get the full air flow. If it's cold or raining, the RT is the way to go.
The S is a bit more nimble, and the riding position is more aggressive, the RT handles well despite being a little more clumsy at low speeds and the riding position is more relaxed.
One thing, whichever model you choose, go for the comfort seat. If you get an RT, see if you can find a Russell Day Long seat. The stock bench seat will kill your ass, and some of the Corbin models are brutal as well. I had one on my S when I got it, and had to get it replaced as soon as possible.