To be honest the Wii era was kind of a bust for Nintendo fans in a lot of ways.

We were always sold this line that with a big userbase we'd finally have all these great third party games, but the system was so underpowered that it got nothing but crappy spin-off games or a ton of shovelware mini-game titles.

Great for soccer moms or if you wanted a weight loss fad, but not really great if you actually wanted to play quality games.

The best Nintendo games for the system, things like Super Mario Galaxy 1/2, Xenoblade, Super Smash Bros. Brawl, Mario Kart Wii, Donkey Kong Country: Tropical Freeze, NSMBU, Zelda: TP honestly would play just as well/better with a regular controller, and even the aiming in Metroid Prime 3 ... Splatoon has shown you can do that just fine with a regular pad.

So essentially that era ended up with Nintendo fans, most of whom had a GameCube, which was $99 by 2003, paying 2.5x that cost for basically the same hardware slightly upclocked, a piddly amount of on-board storage, with a new controller.

And we got no graphics/hardware update for 6 years, being stuck playing our games in SD resolution when most of us had HDTVs for years.

Honestly there's very little the Wiimote actually brought to the table of a Nintendo fan other than bragging rights on internet forums because Nintendo was selling a lot of product to fickle soccer moms/casuals for a couple of years. It didn't make the games better.

Even the whole "well Nintendo will make so much money off these casual gamers that surely they'll in turn spend that money on awesome new studios, like how they used to have Rare in the past!" ... that turned out to be a bust too as Nintendo barely invested in any new 2nd party studios.

Mario Galaxy, while popular, added little more than gravity mechanics to what was Mario 64/Sunshine.

Metroid Prime games played MUCH better without the Wiimote, as did Twilight Princess (can't speak for Skyward Sword since I had fully sworn off my Wii by that point).

As for your list of third parties? MH3 and 007 played better with gamepads. Tatsunoko vs Capcom, a fighting game, definitely would benefit from real inputs. Shattered Memories played better on the PSP (which is just embarrassing) because it had real controls. And based on that list, though I haven't played them, I'm going to assume the others would have benefitted from real controls as well. 

The Wii is easily the worst generation to have been a Nintendo fan. Yeah, it sold well by enticing not-gamers... But at a steep cost. 

We'll have to agree to disagree, since I found Wii to be just absolutely awful. Bad controls, gimmicky games, and what good games there were would have played better with a pad. The Wii itself brought nothing but gimmicks to the table, and while some of its games may have been good, it was stunted as a whole by the console itself. Wii U was a step in the right direction, but it was too little, too late. 

That said, I'm not much more impressed with the Wii U. The Wii U Pad is cumbersome and puts me back in the same "use a different controller" boat I was in with the Wii.