With the stock, you get to use all the S- stuff. With a custom ROM, you will not get them. So it comes down to, if you like to use the Samsung apps or if you want more customization through a custom ROM, but not have the S- stuff.
Incorrect. You can use a custom ROM that is TouchWiz based (Assorted parts of the samsung stuff), or a custom ROM that is AOSP ("pure" Android / Google-released code). You can use custom roms With the S-stuff if that's what you want.