I think that in the third movie ("Spell of the Unown"), the defining moment of Molly's life is when she opts to leave the crystal mansion, bravely facing an uncertain world without the help of the Unown. Her reunion with her parents is important, but it is a further development in her life, not the event that solidified her personality and enabled her to take on the world - she's still learning. In light of that, I don't think she should return in person.
Maybe Molly could appear for a few moments along with her father on TV just as Kenny did in one of the relatively recent Japan episodes (I forgot which one that was, sorry).