Hi Patrick,
The different versions are like an evolution of DMVPN. We don’t really use phase 1 anymore unless you have a really good reason why you want to force all traffic through the hub (security perhaps?). Otherwise, it’s more effective to allow spoke-to-spoke traffic.
Both phase 2 and 3 allow spoke-to-spoke traffic, the advantage of phase 3 is that we use the “shortcuts” so you don’t need specific entries anymore in the routing tables of the spoke routers. I can’t think of any advantages right now that phase 2 has over phase 3 so if you implement this, you probably want to use phase 3.
Rene