The problem with Crystal Skull is not that it uses CG, its that it uses too much. In 1981 they wouldn't use old-school methods of special effects for the jungle chase because that would look like shit, they would instead have to actually go and film it for real and do stunts. Now with CG they just rely on a computer instead of doing it for real--thats the flaw. The limitations of the older methods forced filmmakers to have to actually do things practically, whereas now there is a perception that you can do "anything" because of CGI--but CGI doesn't always look real, so you can't actually do "anything," especially when most of the CG sequences in Crystal Skull could have been done practically. Its an unnecessary use of special effects, I think that is the distinction people have been sensing but unable to realise--special effects are indeed better today, but we use them so much that the older films nonetheless look and feel more real (because they are).
That said, the CGI in Crystal Skull is very tastefully done, except for the jungle chase--thats the most "unreal" part of the film, and its especially frustrating because theres absolutely no reason why it should be the most unreal, they could have easily done it better without using CG and if this movie was filmed in 1981 it would look every bit as realistic as the truck chase in Raiders.