I agree that Padme appearing beside Anakin makes no sense in regards to how the Jedi become Force Spirits. The problem here is that in the OT, the only main character-good guys that died were Obi-Wan, Yoda, and Anakin. Their appearence at the end of RotJ could be interpreted as Luke glimpsing the afterlife, where everyone had a happy ending.

In the PT however, we've got beloved characters dying all over the place. Qui-Gon, Shmi, Mace, Padme, etc. Padme in particular in that her and Anakin's love played such a vital role in the prequels, and of course her being the mother of Luke and Leia. Now we get to the ending of RotJ and see the familar 3 spirits, but what are we to think of the rest of our deceased friends? Are they simply lost to oblivion? If that is the case, it is especially tragic for Padme, whose love with Anakin fueled the actions that lead to both their downfalls. And what good is the afterlife if you cannot share it with those you love most? Star Wars is a fairy tale, and thus should have a fairy tale ending in which the characters live happily ever after, in this life and the next.

So those are my thoughts, but realistically, I cannot see any more alterations being done other than the ones I layed out before (old to young spirits, Qui-Gon), if only for the confusion they would cause.