Whatever you make the title, please at least keep "Indiana Jones..." at the beginning. Raiders is a standalone film, it would just look weird if after two sequels, the format went back.

It depends what is your goal with this fanedit.

If I'd want to have the best title for my vision of the movie I'd call it "Kingdom of the crystal skull", or maybe find another title without "Indiana Jones" in it. "Kingdom of Skulls" is quite good indeed. The audience will learn soon enough about the crystal thing.

To me a fanedit is more or less always a standalone project. No matter how you try to be as close as the other movies of a series, at the end it will be your vision. That's why I personaly would have no problem to cut "Indiana Jones and the..." out. Because, as I said, it would be way to tell the audience: this is my vision.

But, once again, if the goal is really to be as close as the others (meaning that all the cuts and decisions are made with the other movies as references, and not only the taste of the editor...) then, yes, keeping "Indiana Jones and the..." would be a good choice.