Nintendo should use Bioshock Infinite to learn how to make better games.
I will very respectfully disagree with you TC.
1) Innovation in gameplay. I really disagree here. Bioshock's gameplay isn't anything too new, it is mostly just first person action game gameplay. And innovative Gameplay is one area Nintendo doesn't need to work on. Play Luigi's Mansion: Dark Moon, Kid Icarus: Uprising, Dillon's Rolling Western, or Pushmo. And all of those are just games released in the last year or so for the 3DS. Also, I don't agree that want to see it again = better. I don't want Wolf Link again not because it wasn't good enough, but because it was a unique element that should stay unique.
2) Characters. Silent doesn't equal bland. Plus, silent protagonists are common in video games. Link doesn't need to talk, you know everything about him by his actions. Same with Samus and Mario. These are long standing classic characters. Everyone knows who they are and what they're about, they don't need forced "development" added on. Fans don't like it (See Metroid Other M). If you think villains are shallow please look at the likes of most Mario RPG villains, most Fire Emblem villains, Team Plasma and N, or Giygas. Nintendo has popular, recognizable characters; just because they don't have deep-seated psychological issues doesn't mean they need to be redone.
3) Settings. I can somewhat get on-board here, although I think most of your points only apply to certain games. Luigi's Mansion (both of them) has an awesome atmosphere and setting that is very detailed. Some Metroid Prime worlds have great atmosphere. The world of Pikmin is beautiful and detailed and very natural and "alive" Certainly some games could benefit from a more "living world" but plenty are great as is.
4) Story. A great story in a video game is great. However, I definitely am for Gameplay first. Mario doesn't need too much depth and I think this ties in with the whole character thing. As for Zelda, I thought Skyward Sword had a fine story. Again, there are the likes of Fire Emblem, Xenoblade, and Metroid that sort of go against you here.
5) Storytelling. This is sort of vauge and I think the type of storytelling you are speaking of is something unique. It sounds like Arkham Asylum somewhat. This type of thing can't be overused. On a vaguely related note, Luigi's Mansion: Dark Moon really built up King Boo in a great way you have to play the game to see.
Overall you have good, well thought out points. I would actually recommend you just be a bit more specific. Some of these complaints only apply to certain games. Games like Fire Emblem and Xenoblade don't really work for some of these points.
King Boo for Super Smash Bros.
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Silent doesn't equal bland.
It basically does if they actually are silent. Link from TWW isn't silent because of his facial expressions and actions, and Caim from Drag-On Dragoon isn't silent because of his facial expressions and actions as well. Link (non-TWW) is just a boring hero that does what he's told.
And commonality is not a good reason for anything.
FE villians are pretty shallow, just look at the latest entry, Awakening. FE7 and FE8 are exceptions.
FE: Awakening had a pretty bad story, it's commonly agreed on in the forums as well.
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In all honesty, at least in this generation the First Person Shooter may be the most stereotyped and misunderstood genre in gaming(yes, even more then the JRPG.)
Primarily by Nintendo fans whose experience of FPS games generally consists of playing Metroid Prime and watching their friend play Modern Warfare for 2 minutes.
Any Nintendo fanboy who thinks Bioshock is 'just another generic FPS' is really, really, really ****ing stupid. And that's being generous.
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