I can see two reasons this happens. Among some developers I’m sure their is a desire to pad a story and make the game longer. This gives many games, like GTA IV, what I’m going to call a false climax. You have a point in the story where you feel like it should be over, but instead you’re hit with more rising action and another, much less powerful climax and absolutely no resolution.
Other developers, I think want to leave the door open for a sequel and, like in Bioshock, feel like they need to walk readers down that path before the story ends, even though they’ve already accomplished everything they need to to deliver a powerful story. The end result, of course, just waters down the entire experience.
There’s one other reason, as well. Most developers make their game in chronological order. That means they do the ending last. The last thing that gets done on a game is almost always the thing with the least amount of polish and most cut corners — you just run out of time.
Of course, just because you do something first usually doesn’t help either — because at that point you don’t know what kind of game you’re making.
That’s why so many games have great middles, average beginnings, and shitty endings — at least in my experience.