I believe that a lot of the internet criticism pointed at Crystal Skull is just what happens when original films get so beloved: audiences claim those worlds for themselves and decide that they know better what these worlds should be about.
It happened with Star Wars, it happened with Bond and it will happen with the Marvel films etc. Hell, it happened with music’s biggest stars whose later albums became objects of hatred and scorn - just because they did not deliver the rush audiences felt earlier in their lives. Guess what: as you grow older you will view things differently and, yes, become not as fascinated anymore.
I´m not saying one should swallow whatever the artists come up with. But the outrage of audiences, facilitated by the internet, is plain silly. Artists create and make choices. If one does not like them one can be disappointed. But it´s just a piece of entertainment.