You say that you're a fan of the previous three, but then say that Karen Allen can't act worth . So, how can you possibly like the first, Raiders of the Lost Ark, if she has waaaaaaaaay more face time in that movie.
Your logic makes no sense whatsoever.
You had a problem with Indy surviving the blast on a fridge????
What about Indy going to a Nazi rally in Germany, of all places, and getting his dad's book of maps and notes signed by Adolf Hitler himself to get out of a jam??
What about Indy beating the out of a Nazi officer and throwing him out of the blimp only to to tell everyone on the Nazi owned blimp, "No Ticket!!", in English no less?
This is your problem:
You're letting your Christian feeling get hurt.
You love Raiders of the Lost Ark and The Last Crusade because the artifacts in question are part of the Judeo-Christian lore. You can't stand that Indiana Jones isn't chasing an artifact that has to do with Jesus Christ or the ancient Hebrew nations.
That's your biggest problem.
As for the crystal skulls, there's a case to be made for them. I'm not saying that they are real, one way or another, but there's a case to be made.
It's not Lucas' or Speilberg's fault that you can't wrap your mind around it.