I'm of the same opinion. The more effort you put into a game's story, the more potential chance there is that integrating the story and gameplay will be difficult. It highlights a real problem when well-written games are a rarity, but even the well-written ones aren't written in the correct manner (read: to interface properly with the game itself).
I think people need to stop thinking about writing for games as an extension of objective-driven-gameplay, and more as an integral part of the gameplay itself. A few examples of games that I can think of which did this well are the System Shock series and (to a lesser extent, for the reasons below, although it should really be a better example, in ideal circumstances) Planescape: Torment.
The danger is making this statement that gameplay and story (and whatever other elements) are a kind of see-saw wherein you maintain a balance of each one, because that isn't necessarily the case - it's a matter of approaching the situation in a different way. Taking the view that said balance exists by necessesity only leads to people making judgements based on either one critera or the other ("hey, it had no story, but it had nice gameplay", "hey, it had bad gameplay, but it had nice water effects", "hey, it had bad graphics, but the story was cool") - a good example of this occurring is Planescape, which, as I say, should really be the ideal example, but isn't, because the traditional "gameplay" (read: combat) was far worse than it needed to be. There was nothing stopping the gameplay being decent, but because it really wasn't very good, people tend to talk about the story and nothing else, even though the two interfaced nearly perfectly.