Regarding the argument that the “Shaw ghost never existed”, well…the Hayden ghost never existed in that specific form either. He clearly has both arms intact when one should be missing (and yes, both hands are visible in the wide shot). So if the Hayden ghost is okay from that standpoint, then so is the Shaw ghost. Therefore, the “Shaw ghost never existed” argument is no longer valid.
So since we’ve now established this, we can look towards other factors. The Hayden ghost symbolizes regression back to an unstable man who had already begun his descent to the dark side (had murdered an entire village, including women & children). The Shaw ghost, on the other hand, symbolizes growth and shows that Anakin has learned from his past mistakes to truly become a good person in the end. That, and he is the same person (albeit with healed injuries) that Luke just saw behind the mask. So the Shaw ghost makes far more sense, even with the prequels. The only thing the Hayden ghost has going is familiarity with those who like the prequels or saw them first. It was a way to connect the trilogies that doesn’t actually make much sense when you really think about it.