James Luceno does what he can with his adaptation of "Indiana Jones and the Kingdom of the Crystal Skull," based on the screenplay by David Koepp and story by George Lucas and Jeff Nathanson. His adaptation shows why the movie didn't quite work on a story and character level.
Previous Indiana Jones films were simpler. The stories had Jones looking for an object and a renegade faction (usually Nazis) created obstacles to prevent him from finding said object. Or, those factions tried to capture him so he can find the object for their evil goals. In "Kingdom of the Crystal Skull," we get too many characters and a convoluted story. And, due to these many characters and the convoluted story, we get inconsistent pacing.
The 'story' for this particular entry is that Indiana Jones is seeking the crystal skull, an object that will unlock the 'secrets of the world.' There is no clear reason as to why Indiana Jones is directly seeking this object. Yes, he knows the Russians are looking for it...and his 'son' Mutt gave him a note that unclearly links him - Mutt - and Indy's past acquaintances to the skull, but usually Indiana has a definite reason to search for an artifact. Examples: In "Raiders of the Lost Ark," Jones was hired by the US government to seek out the Ark of the Covenant before the Nazis; in "Temple of Doom," he was asked to save Indian village children from slavery and retrieve stones that were part of the same village; and, in "The Last Crusade," Indy is called on to retrieve the Holy Grail by a businessman, who happens to be working for the Nazis.
In "Kingdom of the Crystal Skull," Indy seems to just be looking for the skull just because of Mutt's note. And, he doesn't even really know who Mutt is.
As aforementioned, there are characters that are not necessarily needed. One of those is George 'Mac' McHale, portrayed by Ray Winstone in the film, a character that doesn't affect the plot in a major or minor way. It's not even clear whose side he is on even though it is brought up multiple times and he and Indy have had a friendly history, and this is played into the character as comic relief.
Bottom line: His character didn't need to be in the story.
Professor Oxley (portrayed by John Hurt in the film) is a character that is linked to the crystal skull that is sought by the Russian villains and Indiana Jones. His presence is also a distraction, and much of his dialogue could have been Indy's if we needed to know the history behind the skull and how to find it.
While I don't mind the introduction of Mutt as Indy's son, his character could have been introduced and utilized a bit better. While Mutt knows he's Indy's son, we don't hear about it until later in the story...from his mother, Marion Ravenwood (the love interest from the first Indiana Jones story). He was utilized by the villains to give Indy a note to get him - Jones - interested (?) in attaining the crystal skull. (This is where the motivation of the hero going for the goal isn't quite clear). All Indy knows initially, is that a young brat knows an acquaintance - Oxley - and that Oxley has some connection to the crystal skull.
Some other nitpicks include the Russian attack on Area 51 at the beginning of the story, where they meet very little resistance. You would think that Area 51, holding paranormal and outer space phenomena, would be heavily guarded. However, Russian villains only meet a few guards at the entrance of the facility.
Another nitpick involves Irina Spalko, the main villain. She is described as an exotic individual: pale skin and the body of a ballerina. In the film she is portrayed by Cate Blanchett, and has the potential to be an interesting, mysterious, and exotic character. Unfortunately, she comes off generic. The only thing standing out about her is that she is the first lead villain in the franchise that is female.
Overall, "Indiana Jones and the Kingdom of the Crystal Skull" is a lesson on how 'not' to do an Indiana Jones story.