The differences are semi-negligible. The s2's have slightly more bottom than the s1's (bigger cab, so DUH, of course), they have the ability to handle a little bit more cone excursion (so can handle slightly more power and as mentioned, put out more bottom), lastly, they have a redesigned x-over which smooths out the mids when compared to the S1's. But don't discount the s1's.....they are a great cab! If you're not pushing these cabs continually to the max on an individual basis, then I think you'd be hard pressed to hear the differences in any setting, as you could prob use EQ to make up for the differences between the two series. If you're using one cab, and pushing it the max all the time, then maybe the extra cone excursion and booty of the s2 might be your cup of tea. But then again, maybe the extra mid push of the s1 might be what you need to be heard? When used as a pair, they sound amazing! You can be happy with a pair of s1's, s2's, or blended pair.
PS....physical differences are s2 has a bigger cab (as discussed), redesigned x-over for "smoother" mids, and I think (don't quote me) the main driver was redesigned.....I think....not sure though.....so maybe a PM to Roger might help.