I prefer The Lost Ark over the Last Crusade myself, but both were solid movies. Temple of Doom was also enjoyable (I like all three so much that I have never just watched one, or watched them out of order. Like Ghostbusters, I usually watch them as one long as movie).
Crystal Skull, I believe, was a train wreck. The most obvious problem I found was the Aliens (I liked the whole 'Saving God's Gifts' thing.). But I found the whole movie to be poorly executed garbage, to the point where I can't even really point anything particular out.
This, of course, could just be an effect caused by Shia LaBeouf being involved.
Also, it may just be a trick of my mind, but did anyone else notice that any time in that movie where Harrison wasn't actively talking or doing something, he had a vacant look on his face? Like he couldn't fucking believe he was doing this?