Sorry for the double post (can't edit on work PC for some reason)

The other element that would print money on a console Pokémon would be NFC figures. Popular pokemon from other gens could be 'imported' in game via the NFC. And indeed, that could be how you get your starter. Rather than picking from Prof Oak, you choose which one you want when you buy your game (like the skylanders starter pack).

Pokemon would work but won't happen. GameFreak is too focused on handhelds (pocket monsters!!), even if the Wii U could be a bridge. Having a huge Pokemon game with all Pokemon, regions, online battles is probably what most people would like to have but how many years have we been waiting for a game now that is not about just a fraction of the Pokemon?

Also, Pokemon is turn-based after all so why should a game change it?

Nah. Mario Kart 8 is the game that has the most chances to save the Wii U..  Nintendo of France said that  there tons of potential buyers of MK8 in France, it's the most anticipated WiiU game in Japan and  the preorders are doing nicely according to VGChartz. If MK8 fails then the Wii U is clearly doomed forever.

At least the Pokemon suggestion isn't just pulling out the same tired home console franchises that failed to get GC or N64 into winning positions. But when was the last time a Pokemon game on a home console sold mega millions? Pokemon Stadium 5.45 million on N64. The Pokemon fan base lives on handheld and that's where they want to play.

Metroid, basically the weakest of all Nintendo franchises sales-wise is also an original idea for saving the Wii U, but basically flawed in that it's got pretty much no pulling power depsite being around for years.

So basically neither franchise is a Wii U saving option.

Neither of those would have a big impact. I see only two things that would make Wii U take the sales lead (or come close)

1. A steady stream of interesting titles like DK, MK8 and SSBU, a new IP that creates buzz, big promotion for X and a price cut mixed with a bit of a drought for PS4 and no price cut for XBOne. All of these things have to happen together. I guess a new IP that creates buzz could do it alone, but it would have to be quite the interesting game.

2. Nintendo buys controlling interest in a 3rd party (or 2) and brings their titles exclusive. I mean a major third party, like Capcom, Square or Take2 that has some significant titles with dedicated fans that will buy a system to play it. If, for example, Mario fans AND Final Fantasy fans were buying Wii U's to play their favorite games, the base of users would grow to a solid number and other 3rd party support would likely follow too. This scenario is unlikely.

I don't think Pokemon or Metroid would have much of an effect. Only one drastic move or many consecutive successes will turn things around for Wii U.

Halo 5 and Uncharted 4 exclusively on Wii U would save the system.

If by saving the system you mean the Wii U doing on the 50 million range then I'm sorry to tell you but the Wii U is not going to make it. No game will make it soar, it's destiny as a Gamecube successor is pretty much set on stone.

No, Just no! that would make the current fans don't want the game! We have 718 fucking Pokémon, and you want the game to have less than half? That's why I didn't buy the 3DS Pokémon Mystery Dungeon, you can't limit these things!

Metroid is too niche of a game,

GTA and COD exclusive to WIi U only (not talking about spin off but the main series) would not save the console either because the internet would go into a meltdown and burn down activision and rockstar.

I can understand wanting more pokemon in the game, but isn't the point of MMO's to keep adding content? Nintendo just needs to be VERY open about the fact that there will be all the pokemon in it eventually, and the timeframe in which they intend to release these add-ons. My biggest complaint with his pokemon game (as others have stated) would be making it a, for lack of better words fighting game. Not only have all previous games been turn based, but it feels that turn based is how the World seems to work. Even in the anime, the characters take turns calling out commands to their Pokemon. Turning it into a fighting game would not go over well IMO. 

What is the major obstacles to overcome to get this done?

Well the size of the game for one. This leads to questions like how big of a team would Nintendo need to make the game, and maintain the servers of a game that size. Would it all fit on to one bluray disk? If not would you just have to download the whole thing? If so, they would need to have it come with an external hard drive, maybe pre loaded. I'd hate to have to spend money on an external hd because the 32 GB is too small for the game. Would I? Sure, but it would put Nintendo's poor planning of their internal memory storage front and center for internet trolling.

Now on to the Metriod idea. It's alright. I'd actually like to see another Metriod game like Other M, but evolve the character. Make an Other M trilogy that involves a character arc for Samus that takes her from her fearful and codependent self in Other M and in the second game have her show uncontrollable rage for whoever she's fighting, trying to get over the death of her previous comrades that she has known since the academy. Then in the third game show her mature into the iconic Samus and have her go out with some dignity. 

The major obstacle to overcome with a Metroid game in general?

Metroid isn't that popular... It's just not. And I freaking love me some Metroid.