Dang, I just typed a nice comparison and I lost it. Anyway, in a nutshell the S is quite a bit lighter which is nice. Mine had an unfinished neck and that is something that feels more comfortable to me. I don't know what type of music you play but I play metal and the RG just oozes metal, that is not the case with the S. You can get metal tones out of the S, but it is much easier and better with the RG. With the S I was able to get more rock and hard rock tones. Both had the original pickups at the time. I think all S guitars are bolt on, my RG(T) is a neck through. Can't tell you much about the trem as I had both locked. Compared to other guitars I have played, both the S and the RG play very nice, the neck contour is just right. The pickup switch is accessible but out of the way so you don't knock it. I don't like the neck pickup tones on any of these guitars, I like what I get out of my LP better, but I love the bridge pickup on the RG and the S bridge is OK. I think changing the pups on the S is a must, so plan for that. Changing the pups on the RG may not be necessary, but then that is pretty subjective.
fcarpio's write up is spot on. I'll simply add that I really like the feel of the S Series and the rock tones are terrific, especially through a Marshall. Tuning is very stable and the guitar feels good in the hands.