I don't think I ever played the original, so I don't exactly know how the original two differ. Storyline-wise, I'm very interested to know how they're all different/similar. I wonder if there are any oops type of retconning going on?
Since all three (or four but we don't talk about A New Theory) versions were done by different companies and Falcom's explanation of the Ys games as 'interpretations of Adol's diaries by scholars 1000 years later' allow for multiple versions of the games, there's not much need for retconning in the usual sense. Obviously, some things in different versions simply can't happen if you take all the Falcom-made games together (I'm looking at you, Dawn of Ys' take on the Fact family and the Black Pearl) but Falcom generally doesn't mind the existence of multiple versions of the games from a continuity perspective. Celceta included quite a few nods to Dawn of Ys even though Mask was the one that they declared 'official' prior to releasing their own version, for example.