1) The ending.
Just take a look at what happened to Mass Effect 3, there is nothing like a ruined ending to downgrad opinions about a story. Sure I liked the first chapter of the jedi consular. It was cool to look for the crazy jedi master, and the plot twist in the end of chapter 1, very well done! However, the whole matter of the Rift Alliance is just... boring. It feels like you fly around the galaxy trying to please some whinners, and then in chapter 3 you storm around yelling: "Who is the first son!" Then when you finally find him it is YET another jedi master... Wow, we didn't just spend the whole of chaptor one hunting jedi masters... Furthemore, the whole way the ending is made is significantly less epic than the 4 other class stories I've played:
In all of them you do something epic and furthemore, you leave Corelia and do something "more"
Here are the 5 endings I've played try comparring them to one another if you wish:
And... Consular (yes I'm a pureblood for rp reasons) : http://www.youtube.com/watch?v=sSdcnIYO-NM
2) Getting too predictable
Oh noo! This guy was a child of the Emperor... Oh there is one more, oh guess what that person is... yet another child of the Emperor... How suprising...
3) Too many irrelevant characters:¨
There is so many characters in the this story because there are so many people on your ship after chapter 1. This resolves in none of them getting enough screen time and those they become irrelevant. For instance
4) The Last boss in the consular story feels... pathetic.
I mean to me it felt like 1 storywriter: "Hey the jedi classes should fight the Emperor!" 2 storywriter: "Oh yeah... but only one of them can fight him..." 1 storywriter: "oh... yeah... Then the other one can fight his children!"
I have plenty of other reasons but it would take too much time to write down, these are just the ones from the top of my head.