You dont need to wait for BTS2006 R2 to make this happen.

Basically there are several ways to approach this and one of the main exceptions is that the corresponding BTS WSS Webservice fails when it finds the 'new' version of Sharepoint on the box. (the Sharepoint apis etc. do maintain backward compatibility for existing code)

One technique is to install Sharepoint V2, SP2 it, install BTS2006 and make sure the WSS adapter is working. Then upgrade Sharepoint......fingers crossed.

the other simpler technique is to re-bind the BTS2006 WSS Webservice to work with the new Sharepoint V12.0.0.0 version.

A new member of the BizTalk team Adrian Hamza - elaborates further here