Super Mario 64, Super Mario Sunshine, Super Mario Galaxy and Super Mario 3D World are all quite different from each other. The only similar game is Super Mario Galaxy 2. And I wouldn't mind an HD Mario Galaxy right about now! Just because Nintendo uses the same characters over and over again doesn't mean they don't innovate or change up the gameplay.

Captain Toad: Treasure Tracker is also totally different from any Mario spin-off game we have seen so far. 

Maybe they should have been in that audience xD

Then what vague game is he thinking of? Because the most popular games of the day pretty much ignore story and focus on gameplay.

Same goes for those "same games that appear on every system." Except on Nintendo.

It seems he is talking about the creation process more than the final product. There are tons of Extra Credits videos which go into more depth on how the creation process in games tends to cut out story and how basing a game around a story is a flawed strategy (The one I watched last night was "How to start a game narrative" or something like that).

A lot of writers for games write the same way they would for other mediums, and the story directors try to direct the story as if it was a movie. That just doesn't work from a creation standpoint. The final product may be good gameplay-wise, but the story will be weak and feel stilted because the developers weren't all on the same page.

CoD's yearly installments always get flak from fans for being too samey. Just yesterday Assassin's Creed Unity review came out, criticing the game for not evolving much since AC2 which was something like 6 games ago.

But I believe that Miyamoto was mostly talking about how so many of those games have the same goal: to create something gritty and "mature". That trend is hard to overlook in AAA games...he wasn't saying that they were the same game literally, just that they all seek to fill the same space in the game's industry, they fight over the same space in the market and they satisfy the same need in the consumer. Obviously this doesn't apply to every game, but it is hard to ignore the general trend in the industry to fighting over the same space instead of filling niche's. Nintendo exists almost entirely in the niche, so its hard to apply the same argument to them. While Nintendo iterates on the same franchise, often it is in genres or areas that almost no other big developer participates in.

He was talking about ports. A lot of what Miyamoto said in the article has been said before either by him, Iwata, or Yamauchi.

I think what Miyamoto was stating was the fact that he thought the X1 and PS4 are too alike in terms of their libraries, not that they always put out the same games. That's what it sounds like to me.

I'm not alone in thinking there are people who read the title of the thread/article but not the article itself right?

It was said in an interview by the designers, forgot their names, Bruce and whoever.