I find it baffling that people would accept ghosts, magic boxes and two different religious cosmologies as simultaneously true, but have a problem with aliens (and of course they weren't even aliens). But if it doesn't work for you, it doesn't work for you.
It sometimes feels like half the people complaining about this movie didn't even watch it. The first one was about saving Marion, the second one was about saving children, the third one was about saving his father and the final one was about saving himself. Harrison Ford plays to this, presenting us with a worn out Indy in the early scenes that some viewers then projected across the rest of the film. KOTCS is about that early scene where Indy reflects that life has stopped giving him things and started taking them away. Marion, his father, his career. He's washed up and has nothing to show for his life, especially once he's thrown out of the school. The early atomic scene is a great metaphor for this - he doesn't understand the new world he's in.
The movie is about a second chance, and about the knowledge represented by the skull. Spalko has the exact wrong idea - to her, knowledge will give her country dominion over the world. But Indy is quick enough to realize the knowledge offered by the skull is a trap; the real treasure is knowing that family is the most important thing (symbolized in the film by the way all of the aliens must be in place for the saucer to work). He lost Marion, but wins her back. He lost he son he never knew he had, and wins him back. He helps an old friend (an obvious Brody/dad surrogate) find himself. And then at the end of the film he gets married, with a kid. Instant family. Indy wins. And with that, the return of his zest, which Ford plays up in the latter part of the film.
Yeah, the CGI is terrible and there are some misjudged scenes. But on the whole it's a worthy addition to the series, and the only one to actually wind up being about Indiana Jones himself.