To me the overarching issue is the simple fact that games are no longer typically designed or marketed for gamers anymore, not that this is ultimately a "bad" thing (it can be and has proven to be the case more and more.), they are marketed at the general consumer. Now I don't want to get too far up on my metaphorical high horse (and no it is not made of stars...) but I am sure that is bound to happen at various points through out this post, consider yourselves warned.
I think that the fact that to be a "AAA" MMO nowadays, that you have to cater to the most people possible. It is a bit sad that TOR seems to have been developed for the masses rather than the gamers. I do not mean that as a knock on TOR, but I do believe that games like this could benefit from targeting an audience and going after them rather than trying to sweep everyone under one game. EVE excels at this.
I absolutely love the story in TOR. I love the cutscenes and I love trying to win my conversation choice in multiplayer conversations. I am a big fan of the chosen classes. What I don't like is that we are all the "hero".
In a game like EQ, you felt as if you were one of MANY denizens of that world who were fighting to end (or expand) the evils in that world. I am more of a fan of that than being "The Chosen One". However, TOR does do a great job in the character story of making you feel like the Chosen One.