The last movie's being mediocre had nothing to do with the plot, or the fact that there were aliens. The plots from Raiders, Temple, and Crusade are all just as ridiculous and simplistic. No, the reason Crystal Skull wasn't as good as the original trilogy is because Spielberg isn't the same director anymore. He doesn't have the stomach anymore to direct brutal violence as if it were funny. In the original trilogy, people are getting stabbed, slashed, shot, flattened, chocked, and melted left, right, and centre, and it's brutal, and it's violent, and the whole thing is being done for laughs.
But, post-Schindler's List and Saving Private Ryan, Spielberg has clearly changed his opinion about filmic violence - he now feels he must treat the violence seriously, which is why we get seriously violent movies like Munich and War of the Worlds. They're brilliant movies too, but they don't treat death and destruction as a punch line, as the old Indiana Jones movies did. Those older movies are made by a man who thinks he's immortal, and that murder and death can be funny. He's outgrown that part of himself, and to continue to make Indiana Jones movies is to pretend he has a youthful callousness towards violence that he no longer has.
So, in Crystal Skull, Spielberg, as I said, doesn't have the stomach to poke fun at real violence. He could have therefore taken the violence seriously, as in War of the Worlds, but this is Indiana Jones - it's supposed to be light. So, as a result, the death toll is lower, the special effects are less convincing, the jokiness is at an all-time high, the villain is more misguided than hateful, and the violence is extremely light and cartoony. He basically chickened out. He is too aware that bad guys are people too, and that they have feelings, and that violence against them just isn't funny. And he's right about all that - but it makes for a very timid action movie.
What I'm saying is, any new Indiana Jones movie is going to have the same problem. He simply doesn't think death and pain and destruction are funny anymore, as he did back in the 80's. As a result, his Indiana Jones movies will now always have no teeth. They'll be jokey and silly, and they won't have the guts to be brutal and exciting and violent anymore. Unfortunately for the Indiana Jones trilogy (but fortunately for movies like Saving Private Ryan and Munich), the man has grown up.