I don't know... people keep saying they should have just made it obvious... How much more obvious could it have been? The emphasis on the whole Shar/Selune dichotomy, the fact she is a follower of Shar... And she has this weird artifact that is clearly massively important to her.
It's kind of like that whole average character thing... They gave us all these choices and we still manage to be as vanilla as possible. They put something important in the game. That thing is really, really difficult to ignore. And they made it even more obvious as time went on... At some point, it's incumbent on us to pick up on it. I feel like we're complaining about them giving us entirely too much credit.
I feel similarly about this to how I feel about the Grove/Goblin routes, there's a clear way that a reasonable character would choose, people who don't have Shadowheart on board are probably making a point of working against the game. I would guess that these are all problems for after your first playthrough.
That still doesn't excuse writing yourself into a corner like this though, especially when you're making a game that is up-front about choice and consequence.