The problem with the Crystal Skull was that it completely BROKE the Indy Jones film structure. The idea is that Indiana Jones is thrust into a situation as a skeptical scientist, and in the end your suspicions are confirmed that OMG MAGIC IS REAL. The entire structure of Raiders and Last Crusade (and Temple of Doom, in a weaker sense) hinge on the progression from the realistic to the supernatural, and as Indy gets closer and closer to the MacGuffin, the progression becomes apparent, until the climax when you find out what the deal really is. I was rolling my eyes before and after they nuked the fridge, simply because everything up to that point was Hollywood retarded to begin with. The sheer scale and flashyness of the opening sequences completely misses the mark of pulp adventure and aims at high-action, scorning original Indy films were based off of, and the result was something I'd rather not think consider as Indy canon.
Even as a stand alone film it wasn't much better than Transformers.