I really don't think there are many differences between the 2.
UIS1 works well with some programs and is faster. Runs more like the original explorer window pane from what I see.
UIS2 has more options and can be more 'animated' than UIS1. It can have more room for imagination than UIS1.
I'm coming up with some stuff in the next 3-4 months

, that to me basically calls out my points. One will be very artsy and use allot of transparentcies and maybe some animation on selected areas while the other (the same idea) is more confined to a specific area with animations and transparentcies.
Take a look at BlackComb for Windowblinds. It uses both. Then look at only UIS1 skins and then look at UIS2.
Another good example is Combat Flight Simulator by The Skins Factory. They use both UIS1 and UIS2.