I was tempted myself to give a couple of months after the SGSII release to see if there was any new word on the Prime because I like vanilla a little better. The more I thought about it the easier my choice became. Every Android phone I have had has been rooted. I plan on doing to the SGSII as well. All of my phones have vanilla 2.3, even my old Hero. So updates arent really a concern since we have some amazing developers on all the phones.
That being said it will probably be easier to compile stock Android for the SGSII than to port TouchWiz to the Prime. I like the ability to have more options on what ROM I want be it vanilla or TouchWiz.
For those that are waiting a for the Prime because of "better specs" I hear the Nexus Z42 is going to have an octo-core processor with a terabyte of RAM...
Sorry for the long winded post