The FBI giving Indy a hard time after the area 51 incident. Despite one military officer vouching for him. Apparently Indy was in the service and eventually obtained a Coronal rank. That wasn't good enough because his friend was a commie supporter. Him loosing his job or forced to take a leave of absence was not needed. There was no long term consequences after the first act and by the end of the movie he was an "Assistant Dean". How this happened or why this didn't happen earlier is beyond me.
The Aliens at the end. I didn't hate them, but just wondering what was their point in the movie?
Irina. Did she have psychic powers or just

ing with Indy? She wanted all knowledge from the aliens but ended up being dissolved/transported to the alien ship.
The crazy old guy knew a lot more about the aliens than realized.
Mutt being Indy's son.
The scene where Mutt picks up the hat and is moments from putting it on would have been a perfect opportunity for Indy to give him the hat as a passing of the torch but for him to take it back was just sad.
What happened to the classic Indiana Jones logo??!??!?!?! Instead we get a generic title card.