I recently purchased these sets to expand into being able to have a full wing of six. These cards are definitely different from those printed into the original boxes. That said it is easy enough to have these purcahsed cards replace all Grace, Intelellect, or Strength cards that a player woudl need. The issue would come in with the addition of the trait cards.
The last time I played Phoenix Dawn Command I used a Rank 3 character with a mix of old and new cards, and given that the split was fairly even it wasn't easy to tell what I woudl or wouldn't pull based on the card difference. If only a single card were replaced though it would be very noticeable.
The additon of the new traits though is a definite Pro to purchasing these sets, as any new/additional material is great to have!