Yes Puppets look more realistic, and you can even fit them with mechanical joints and rivets so they can move, example most of the dinosaurs in Jurassic park, CG was fairly new at that point so they had to make the best out of the puppets.
But on the other hand with CG, in a few more years the artists can figure out ways to make them look and animate a little more lifelike, the only thing CG has over Puppets is, they have a large amount of freedom to make the Character do what ever he pleases, as the CG character does not exist in the real world, so if the team want the CG character to run off walls, fly, do some crazy ninja ****, the artists can animate it to do that.
with puppets, for the most part they are stationary.
I side with both in a way, But CG will soon take over, fivin a few more years time, actors could well possibly be put out of jobs.
Making a CG movie alone will cost less in the future, as you don't have to pay actors ridiculous amounts of money, and you have full creative control.