For example: The CGI Jabba in the SE of ANH. I am not really against showing Jabba, but in 1997 CGI just wasn't advanced enough, and It makes the scene very distracting, especially when Han starts clipping Jabba. (After he walks behind him. He leans toward the actor, but it is too far for the Jabba model.)
CGI free's filmakers up but it can be overused. There was no reason to have the droids in Dexter's Cafe in AotC made of CGI. And Yoda being CGI is pointlessly dis-continuous. Yoda's skin isn't supposed to be that shiny, and he isn't supposed to be able to move that much.
And it probably wouldn't bother anybody if he had been CG from the begginning, (If the technology existed in '79) but the Puppets look so different it's hard not to notice.