They are really moving with the virtual thin apps here and we saw a few issues around IE6 with some apps (I was told appv can't virtualize ie apps which is why they lean towards vmware).
The more I get involved the more i can't help but feel that we are losing something when we move to sccm 2012 because of the seemless intergration. Even the packaging tech they are using is more of a mystery to me.
