The problem is with an attitude like that nothing Bioware could have done would be acceptable. In the end it is their story and not yours. You were able to influence that story to a degree with your choices but are still playing within their story. They brought it to a conclusion and there really aren't many good ways to end it.
Would you rather have had the Crucible just blow everything up? Not activate? What? The endings aren't bad piled on top of bad.