Flaws are inherent to storytelling. No matter how good of a product you produce, there's always going to be something wrong with it that some folks will demand that you be hanged for. Sometimes it's a bit of character writing, sometimes your pacing is just too off for some people to be able to deal with. And sometimes you screw up big time with your story by lagging on a non negotiable aspect of the story: the ending.
Whether you're talking about books, movies, or in this case, video games, the ending is considered by many to be absolutely paramount. It's the last moment we're getting to spend with these characters and this story, so you'd best make it memorable. In the case of video games, this is even more daunting since you not only have to make it satisfying from a story perspective, but gameplay as well.
Sure enough, not every game gets this right. But what about those games that had you hooked right up until the last moments when it completely lost you? What about those terrible endings to otherwise stone cold classic games? Well, then you get one of these very unfortunate cases of leaving your audience with whatever the video game equivalent of blue balls is.