Deus Ex also comes to mind, since there was one on the WiiU.

Paper Mario
Some Co Developed sports game from EA and Nintendo.
More art style like games (less demanding) exclusives from third parties such as Ubisoft. Why has there been no follow-up to the success story of M&R: Kindgom Battle? Or a more colorful take on Call of Duty like game setnin a fictional world?

Why hasn't Tencent convinced Nintendo to allow them to develop a Nintendo Moba?

Why isn't there a Nintendo first Party Diablo-like game yet?

Why hasn't Disney put the one star wars game that would do well on Nintendo on it with Rogue Squadron 4?

The only way to improve 2d stuff is redrawing it. So 2d games can only be remade, not remastered.

GTA V, a remastered version should be a breeze for the system, and it would sell..it would sell a lot. On a personal note Call of Duty. A remaster of Black ops is sorely needed for mobile online play.

Tekken

XCOM

Guilty Gear

King of Fighters (IV / V)

Only...

Don't know why people are saying Monster Hunter when Generations Ultimate is on Switch.

Biggest surprise for me personally is Pikmin. I'm not a fan of the series, but Pikmin 4 was announced 5 years ago now and 3 should have been really easy to port, so it being a no-show is pretty surprising. Series like Star Fox and Paper Mario came our late in the Wii U's lifespan and had pretty mixed reception, so I wouldn't have expected them to show up before now.

Etrian Odyssey, XCom and a new Monster Hunter (there was only the port from the 3DS version).

2D stuff can absolutely be improved with no redrawing.  Take a look at Smash Melee running on Dolphin. Nobody redrew those models.

Also, remaster does not strictly refer to visuals.  You can leave the visuals entirely alone and rebalance the gameplay, fix bugs, change the audio up, or otherwise improve a game while leaving the original source code mainly in tact. 

i will take GTA: San Andres for switch in a heartbeat!

As far as 1st party goes, personally I feel the biggest franchises not covered yet are Tomodachi life and a Wii/Switch sports/series reboot/remaster or whatever they decide to brand it as.