Nintendo approaches game design very differently than many other companies which is why their games so often are so revolutionary and have such simple stories ...
Nintendo starts where other companies finish by focusing on the unique and interesting gameplay elements and then working their way backwards towards the story line; Mario Galaxy was developed first by figuring out that it is fun to platform on planetoids of various sizes, to play around with gravity, and to use a wide variety of special powers (Bee Suit Mario, etc.) and then figuring out how Mario was going to be put into an environment which has these things.
Nintendo is also very restricted in what they can do being that they have spent over 20 years defining characters and now everyone has expectations about what they want; most series that have been around for as long have just as shallow of characters, and as just as "vapid" of storylines (yes, Metal Gear included). There is a definite benefit of being able to start a new series today, without any preconceived notions of what the characters are supposed to be like or how the story should be told, if you want to produce a good story in game ...
