The whole aliens thing in Indy 4 is not consistent with the other films. Forget about all the religious points in Indy 1-3. The original films were more about human interaction, history, mytisism, it had a magical feel about it. Throwing in aliens into the story took all that away. Why do you think it was poorly critiqued. It was not a good ol' Indy story. Rather it followed the lame "let's throw in a bunch of crap into the movie because it will look cool" hollywood idea.
The aliens was not the only problem with this film as I mentioned before. But it was the biggest problem.
But going back to the religous tones in Indy 1-3. What's wrong with continuing that story line? All three movies had to do with a religion. The 1st was mainly Judism, the 2nd was Hindu, and the 3rd was Christian. Indy 4 could have easliy been about a Mayan religion (which it started off as) but then the whole alien nonsense screwed up the entire movie.
There could have been so many avenues the story could have taken but Lucas wanted aliens. The Chrystal Skull could have been a key to the City of Gold, or an ancient weapon, or the secret to immortal life, or the world's greatest secret, or something! Nooo! It needed freaking aliens....
Lucas had Star Wars and Indiana Jones as 2 separate genres. One was the Sci-fi, aliens, space ship genre. The other was the adventure, world traveling, nazi fighting genre. It showed that Lucas was able to be diverse in his storytelling. But when then aliens appeared in Indy 4, to me, it just made Lucas a one trick pony. ALL ALIENS ALL THE TIME!
Seriously, wouldn't it been nice to watch a Lucas movie that had nothing to do with aliens? Don't get me wrong, I like Star Wars as much as the next guy but come on!! Give us a break! What's next? Indiana Jones piloting the Millenium Falcon!... uh...er...wait a sec!