[Tyhm]

Play out the first part of that diatribe in text in the intro, about how they conquered worlds and stuff, Metroid or StarWars style...then work a cutscene where the main characters (not necessarily the player - establish the support heroes early on, the captain, the rebel, the mechanic, the admiral) rush a group of characters, including the created player, onto the phaseshifters...player regains control on the new ship, and whoever's there to greet them is there to greet them.
Maybe they have a scripted battle where they fall back to the phasers, to learn the controls on the fly...you know, like in Super Metroid where you fight Ridley or Ripley or whatever that purple guy was, and no matter what he flies off with the metroid...like that.