It's hard to make an Indiana movie featuring a very old Indiana and then using him as a second banana to bring in Wombat. That was the main problem with his. What they should have done was just spin off from that and introduce a new protagonist.
I think one problem with that is that even though Crystal wasn't very good in terms of content it performed well in the box office and was probably still recognized by some of the younger viewers, so producers probably figured that they could still milk more out of Indiana's character while slowly transitioning to a new protagonist. Meanwhile, FWIW, they did that with the TV series, and retold that part of Indiana's life briefly in this new movie, plus start it off with context from the early movies. In short, they were borrowing content from earlier works, assuming that using the same formulae would still work for this new one.
Also, it was sad to see several of the protagonists seemingly forgotten, like a professor who's about to retire from a city college and a friend who's now a taxi driver. That plus weird secondary characters didn't help (like the black antagonist who doesn't look scary and appears out of place), as well as other weird scenes, like Indy running like a cartoon character on top of the train carriages and the Nazi soldiers saluting to their superiors when a locked door was opened.
