I think maybe you're getting out of it what you put into it. I mean, if your problem with the story seems to be that missions can all be grouped into "kill", "collect", or "deliver" then I think you'll find that accurately describes every mission in every game you've ever played (even ones that are considered paragons of storytelling).
Engagement is a very personal thing, so maybe the correct complaint is just that you're not engaged by this particular story, so let's narrow that down. Maybe you just find it difficult to empathize with any of the characters, or you simply find them unlikable? Are you concerned maybe that your choices aren't making a difference to the story? Is it that the nature of the genre (being an MMO) means that you can't fail, and that you'll be delivered to the end of the story one way or another, no matter how much you invest into the characters?
Those are all valid, but I figure we should zero in on it.
I think what you are saying is more accurate. I just do not like the trooper story so I am probably not making any attempt to get into it at this point. I was hoping for someone to maybe say "Hey I didn't like it much either, but check this one out". At least it seems like I am the minority and the story thing is not as bad as I thought.