Of course, Livy was writing some 130 or so years after Polybius. Where did he get his source material on earlier military organisation from?
Plutarch and Dionysius are both later still.

As it is, I rather suspect that both spears and swords were present in both the historical hastati and Gaesatai formations. Did not the later 'sword-based' legionaries use pilae as spears when necessary? And the Gaesatae were simply Gallic mercenaries from what I make of the sources (Polybius again); there is no reason for there not to have been several types of weapon in their repertoire.
However, the game engine prohibits the use of more than two weapons per unit. So herein lies your dilemma. As it is, I would personally support the use of spears by the Hastati as the first (less privileged if not actually poorer) rank and swords by the principes. But the EB team decided to follow Dionysus in making them spearmen. Since he was so much later, the persistence of spearmen when all legionaries carry swords might have the ring of an older source.

You could equally argue that young hastati are less familiar with battle and more inclined to blindly follow 'the glorious ways of their forefathers' who were spearmen, while the older principes aren't quite as naive and know the value of a good sword in close combat.