The S I sleepers have a small closet that's usually too small to put anything in. S II sleepers have a recessed wall where the closet would be, accessbile from the side, and it's easy to store a small carryon bag there. Also, on the step side, the S II steps blend right into the wall, meaning you can put small items there (papers, coins, keys, pens, etc.) without a problem. On the S I sleepers, there is a gap between the steps and the wall, large enough for something to fall into, but too small to get it out. That reason alone is enough to have me prefer the S IIs to the S Is.
Also, if you have electronics with an AC adaptor, the plug on the S I is recessed a bit, below a large dial of some sort (I think the heating controls), making it difficult to plug some things in. On S IIs, the plug bulges out a bit, making it more accessible.
There are a few other differeneces that I can't think of off the top of my head. I think the shower might be different, but I can't recall exactly how.