The rules state that one should "use both new decks instead of the Stage I and Stage II cards provided with the original game" (SE page 9).
I don't see why one could not mix the old and new Stage I's and II's?
Presumably, the "conflict encouraging" aspect of the new cards will go to waste upon mixing with the old ones. On the other hand, when combined with the Age of Empire variant, a mix of "war" and "non-war" objectives sounds appealing.
Sounds tempting, especially if you were playing The Long War. I think more unpredictability in objectives is good - I'm surprised FFG just created a replacement deck, rather than supplemental cards.
You know what might be fun? Before the game, each player chooses 2 Stage 1 Objectives, from either deck. (Start with the speaker, go once around the table, then backwards, like building the galaxy, until everyone has chosen 2 Objectives.) Take those 10/12/16 objectives, shuffle them together, draw 6 (or however many for Long War) and use those. Do the same for Stage 2, but with each player only choosing one objective.
I'm interested in this, myself. Do many of you keep the objective decks seperate entities like the SE rulebook says or do you just go ahead and mix them up? If you keep them seperate, do you just play one type depending on your group's mood?