I would have liked to get rid of Amarant just because I found him annoying =P And I don't think he would be missed much. I would have liked a more warrior type character too maybe, in place of him or something.

And maybe Garnet could have had all the summons and Holy so it would be easier to choose between her and Eiko in the final battles. Although I guess it was a good thing that they had unique summons and abilities.