I suggest visiting Peavey’s website and comparing the specs for the two amps side by side. Here are a few differences I think are important:
The front panel for the VIP 3 is more advanced. It has an LCD display, so you can clearly see what effects and models you are dialing in. I like this feature in modeling amps. It gets a little confusing trying to figure out which knob is doing what, and the little display can help.
The power rating is another major difference: The VIP 3 is rated at 100 watts, and the VIP 2 at 40 watts. While the power alone may not be a deciding factor for some guitarists, for others power should be a consideration.
For example, if I were going to play in a band, I would definitely prefer the VIP 3. I would want the volume and headroom that comes with 100 watts. On the other hand, if I never intended to take the amp out of my house, the VIP 2 is certainly loud enough.
However, even for home use, I may prefer the VIP. It has a variable power feature, so even though it is rated at 100 watts, the PowerSponge lets you dial it back as far as one watt. This, in effect, is like using a power soak on a tube amp.
The cost difference between the VIP 2 and VIP 3 is about $100 at the time I am writing this. However, remember that you may want one of the (optional) Sanpera pedals to control the amp, so factor that into the cost as well.