While it would be great if every decision our toons made had a lasting impact, it's logistically impossible. Between the eight classes and the number of quests available, we're talking about a near infinite number of possible realities; it simply can't be done. Now why should the advanced classes have different stories? Taking the consular for example, you are the ONLY Jedi capable of curing the plague affecting the masters; this story is established before you even choose your advanced class. The AC determines your style of play, nothing more. As for not getting experience in the phase with your friend of the same class, it says plainly that only one of that particular class is allowed per phase. This was put in by BioWare to slow down the leveling process and prevent 4 friends from speed leveling their same toons.