Yes, at almost any point in the WC arc, you could reintroduce and follow someone/something else as the story evolves. Recall that WC2 shows us the Third (?) enigma campaign. Why not present the option to fight the first or second enigma campaign aboard a different ship?
On a different thought: take advantage of the internet... release the game with WC1 ships (hornets, raptors, scimitars, rapiers, exeters, ralaris, fralthis, etc) and then, as the player proceeds and improves, have the game tap into an online server to introduce some WC2 ships and weapons. There's no reason each chapter has to end with "and we'll see you again in 10 years..."
It'd be interesting to watch the introduction of new ships and technology from the frontline perspective. What if you flew a mission and encountered the first Kilrathi ship (say, an early Ralatha) with Phase Shields. You're hammering on it and hammering on it and...it's completely unharmed??!
That could be an entire branching arc within the story... following along as your air group reels from the encounter and has to fall back on your carrier and escorts, hoping that their heavier weapons can do the trick in time.
...and that's not even getting into the opportunity to do another stab at a WC
riv type game!