Based on folks on the Naim forum who have compared both, more people prefer the Supernait 3 over 2 while a few prefer the 2 over 3. The 3 was claimed to be slightly more clean and detailed than the 2. The 2 was said to have more weight and drive in the bass, more of the "typical" Naim sound.
There isn’t any consensus whether the Supernait 2 or 3 will sound better when used with the power supply (Hicap DR). Although there are few who prefer to use the Supernait without the power supply, there are many who run the Supernait with one.
The 3 has the built-in phonostage which will be useful to some people.