I think most people will agree that the VV games have improved with each version. The graphics are better, little glitches have (mostly) been ironed out, villagers have more varied and interesting actions, and so on.

I prefer playing VV3 for these reasons, although I enjoy playing both VV1 and VV2 every now and then, for a change. Of course, once VV4 is released (it's currently being developed) I'm sure that that will be the best-ever!