I would probably say the single biggest alteration in KQ2 plot was probably the switching of the monk with the vampire character.
That is in the original King Graham and Valanice was married in the monastery by the monk. Graham had killed Dracula earlier in the game.
Whereas in the the unofficial remake, King Graham and Valanice are married in castle by the vampire Caldaur. Graham kills the monk earlier in the game.
The reason why Father isn't nearly as big of a change, is that his addition mostly involved in the ending of the game. He also was "tied" into the beginning of the game, although that isn't clear from the beginning.
He doesn't have that much involvement during the middle of the game except for a small extention to the mountain top "gem" puzzles.
While keys became gems in the remake, that isn't that big of a change, as they pretty much both share the same exact use.
I don't find additions to the plot to be that big of a change, as long as they are only additions that expand on the original plot and don't alter the events of the original plot into something completely opposite of what originally happened.
Whereas switching the characters around, and turning characters into opposite of who they originally were, so that those who were once good guys become villains and bad guys become good guys is a huge deviation from the original.
