They don't give enough customization. Main characters that are created don't have to be horrible. Mass Effect, Dragon Age, Baldur's Gate, and Neverwinter all do just fine. The difference is, they all allow extensive customization of your character. Appearance, background, in some cases personality, race, etc. They also have branching dialogue options. Something that if IS wants to continue using the avatar, they really need to adopt. They also don't have a story completely based around them. There are other things going on in the world. More than just the created character are competent enough to handle the situations at had. I think Awakening was a good start for the MU, central to the story, but at the same time not being constantly praised.
I think if they want to make it better, improve on the appearance customization. Really make it where players can create the character they want. Example being in Fates I won't be creating my Paladin that I create in every fantasy game. The customization options just arent there to make him in this one. Also allow more control over dialogue. If they don't want to go with dialogue choices, then at least allow different personalities that effect what they say, do, and act like. That and they really need to drop the praising of the character. You don't have to make him hated or dislikable, but make it where he isn't the constant character that from the time he was 5 he was told that he is the hero of this land.
I also think dropping the Otaku pandering could help. With the personality system I stated above, it could also decide what characters can be supported. Stop the entire full cast support and limit it. That and I think the entire reason for the constant MU praise in the story is because of Otaku pandering. They try to hard to make the player feel special, instead of making a good story around the character they created.