Nintendo doesn't like to focus too much on the storyline, because the storyline doesn't sell the game, the gameplay does.

Nuff said.

I agree with this. Some games, such as Twilight Princess, just feel like they are thrown completely out of whack due to the addition of tutorial stages or introductions to the controls. In the case of that game, we know this was something that was added late in development in order to help familiarize players with the new wiimote controls, and that's also probably why it feels so out of place in the game.

Many Nintendo games (Mario platformers especially) do a fantastic job of introducing you to the gameplay in a way that perfectly integrated into the experience. You learn as you go along, and the whole thing flows naturally. But this is something you really have to take into consideration at an early point during development or else you don't end up with a homogeneous experience. If you are going to add an interactive tutorial late in development, you are better off having it as a separate section of the game, like they did for the VC release of Sin & Punishment. It gets the player up to speed but not at the expense of the main event.

I think the same goes for story, mostly. If it's not an integral part of the experience you are better off sticking a screen at the beginning which says:
"In the year 2112 the earth has been invaded by evil forces.
Journey to neighboring sectors destroying invaders.
You are Mach Rider!" LOL
There's nothing wrong with admitting a certain aspect of the experience adds nothing to it and relegating it to the side in order to focus on what's important.
And if it is an integral part of the experience then it probably deserves more than a few lengthy cut-scenes that break the flow and immersion of the game. This is akin to pausing the game to tell you about the controls, as TomaTito already said. It's ok when done in small doses to add clarity but other than that should be avoided whenever possible.

The thing about Other M in particular is it feels like Nintendo thought it was really important for the continuation of the franchise to fill in these "gaps" in Samus' character. Unless they had very specific ideas in mind for the next games in the series, I am yet to understand why this move was so important at this stage... then again I haven't played Fusion so maybe it holds the answers that I seek...

For me it usually HAS to be in the game otherwise i won't finish it. It doesnt have to be an amazing story, just one where i care enough about the characters. If it does not have a story, it has to have a multiplayer competitive aspect to it. Ill play any game, but i just lose interest to those that dont have anything.

But they could have just as easily inserted games into the time-line without exploring Samus' character, like in the Prime games. Maybe their "plan" (not that I'm sure they actually have one for this franchise) with Other M was to introduce Samus as a character instead of a suit, precisely in order to facilitate this transition to a new look in games following fusion. Had the personality they created in Other M been well-received, they could have gone on to make a game in which Samus has the same personality but only a different look, thus preserving continuity in the eyes of the audience.

Then again it's just as likely (if not more so ) they are just doing whatever they want with the franchise. I mean it's not like they have a clue what to do with StarFox or F-Zero for that matter.

Tagged for later. Gonna read all the responses later.

Read books, not just manga weeaboos, Books.

as far as metroid even goes, they could always just write off what happened or say samus got clones or anything to just do away with anything that would lock up the story. they can also just put a little blurb in the manual and have the next game be a classic style metroid where samus gets a distress call and explores a new planet. they are hardly constrained by the events of fusion because they are nintendo, write if off as if it never happened and follow up with an awesome new game.

the one thing that really pisses me off is this gen nintendo has just shown glimmers of how awesome they can make their franchises. nsmb wii is the best realization of all the new things they can do with, imo, good motion control involvement, great gameplay with fun powers, enough processing power for lots of enemies on screen, which i love, and enough power to artistically represent the levels without being restricted. i just got to the part in other m where you go through the bridge and see the two dinosaur looking things, and those parts where youre not being told what to do explicitly and you can just play are really fun. its just wrapped up in a terrible plot that breaks the flow of the game too many times.

Not really a good reason to completely ignore an important aspect of a game.

but the thing is, story really isnt an important aspect of the game. its game, not a book, gameplay is king while story is really unnecessary, especially for nintendo titles