I've been mulling over the idea of class stories for SWTOR for some time now. I'll get all of my praises out first: It will make leveling and interesting and fun experience for the player, it does an excellent job at breaking up the grind by making players make meaningful choices that don't involve which boar they should be disappointed in next for not having a liver, and can make even non-roleplayers have an idea of who their character is and possibly introduce them into that hobby.
But what about story consistency?
Most of us are aware at how quickly player victories are turned into the victories of major NPC's or how nobody can ever remember our names despite us being around often enough for them or be remembered. (Varian killed Onyxia, Tirion and a nameless group killed the Lich King) But these little parts were there for a REASON. The choices were taken out of the players hands in order to create a story that made sense and was cohesive.
Give players choice in how a story progresses without actually having the world progress with it lands many players in different places. Which makes players create big grey spots in what is going on in the world, especially when it comes to Flashpoints. Let's use two on SWTOR's site as an example.
A Sith Flashpoint gives players the option to let a captain who had disobeyed orders to live or to kill him off for disobedience. This is the captain of a battleship, and because of this Bioware can't touch the NPC in any way outside of this Flashpoint. Is he dead or alive? What were the repercussions of either decision? They can't do that without having all these different diverging threads that need to fit in to the game world. Another involves the Republic rescuing a Jedi from a prison. It's important enough a mission to warrant sending players after it, but then we have a break in story where the outcome is once again hazy.
As I've been briefly mentioning, there seems to be two ways to go from here. The first is to consistently make diverging threads of plot, which would be too much of a mess for any company to handle, especially since Flashpoints are the equivalent of dungeons and can be run over and over again. The second is simply to make any and ALL player decisions either so minor they can't affect the overall world/universe or those that do have a major impact have hazy after conclusions.
And then we have future content updates. I don't doubt it will be a bad idea to keep introducing NPC's to kill off or spare constantly, as it is a big universe, but sooner or later our plot decisions are either going to feel incredibly minor or they're going to run out of major NPC's they can even use. Bioware really has to walk on eggshells here in their writing, or else major characters will have to be written out on the sole basis of ambiguity in their fate.