It's a thankless lot in life being a gamer who cares about stories in games.
With the rare exception of companies like Bioware, most developers tend to see story as something of a weight around their necks - an unpleasant task that must be endured, like paying taxes. Many developers put story dead last on the priority list, changing it as many times as needs be, ostensibly for the sake of the game - even if the story itself ends up as meaningless garbage as a result.
You can see the results of this in the stories that populate modern gaming. Most of them are, to put it bluntly, wretched. And that's an inevitable consequence of the lack of respect paid to them during the development process. If you don't put time, money and effort into QA testing, you'll end up with a buggy game; if you don't put time, money and effort into the story, you'll end up with a derivative, nonsensical experience. It doesn't take much to figure that out.
Ironically, this approach often ends up hurting an otherwise good game much more than either diverting resources to the story, or just abandoning all pretense of story, would have done. There is nothing quite so bad, nothing that sticks out so poorly, as something that is done half-assed. Red Steel's cardboard cutout cut-scenes, Gears of War's "what the hell is going on here?" confusion, and Army of Two's mindless profanity-filled dialog are just a few examples that spring to mind from the last few years.
Ultimately, these games would have been much better off without any story at all - to have, like the 8- and 16-bit games of yore, a piece of text at the start explaining who you are, and an end screen when you complete the game. To be, in other words, nothing more than a game. Think about it this way: Dead Space attracted only the mildest of criticism, if even that, for being a shooter that had a rigid focus on single player in an age where a multiplayer component is starting to be seen as a shooter staple. Would it have been a better game with an online multiplayer that was utterly basic and broken to the point where it was unplayable?
Of course not. It would add nothing to the game and only give reviewers an area to criticize. In just the same way, poorly-handled stories add nothing and risk detracting from everything. You may not miss the water until the well runs dry, but if you never had a well in the first place, it's a moot point.
Yet having crafted a half-assed story, developers resent that the reviews of their game often detract points for the wretchedness of the story. And so the cycle repeats itself. Story and gameplay come to be seen as enemies, where one must be sacrificed for the sake of the other. Braid creator Jonathan Blow reckons that story and gameplay cannot peacefully coexist, stating that "even if we had really, really good writers [writing game stories] it's still really hard to do a good story in a game, because of the game part".
A recent, and otherwise excellent, article at Gamasutra listed giving priority to story as one of the most common pitfalls in game design, as if you have to choose sides. It is as if there are only two ways to think about this issue: either story is the beginning and end of gaming, or story is a throwaway piece of nonsense to be added in only to tick off another box on the PR sheet.