I don't think they should allow flying right away. It just gets too complicated to make quests interesting (trying to make the skies not so friendly or something) when anything that doesn't require killing massive numbers of an enemy for drops or shear numbers amounts to flying just next to the objective and killing a couple guys to get to the goal.
I do think it would be fine to do the tomes thing. No content is really "immersive" for alts anyway, because it's you doing something you personally already know was done before. I actually really liked that.