Personally, I think Beyond Good and Evil 2 would work really well as a Nintendo exclusive, and the reason for that is:

1. Nintendo needs more games between their first-party releases.

2. Ubisoft doesn't seem to care about it at all, they keep promising it's being made but it has been what, 8 years since they announced it?

3. They could easily port the HD Xbox 360 version of BG&E and bundle it together with the new game, just like they did with Bayonetta 2.

4. I feel like it fits more with the Nintendo audience than it does with the Sony/MS audience, mainly because of its artstyle and gameplay, so it has a chance of selling well this time, especially if marketed right.

5. It's a game that could actually have a use for the GamePad, seeing as the camera mechanic was an essential part of the first game.

What about you guys? 

Starcraft: Ghost

Fire Emblem Warriors

Half Life 3, of course.

You just had to be that guy, didn't you hahahaha

Vanquish 2

Well, you used Beyond Good & Evil 2 in the OP and Shenmue 3 and FF7R are already being done, so no choice ^^. And HL3 could fit with 4/5 of your arguments ;) 

capcom to make another Mega man game. The megaman game also has a special Nintendo section in it. Where there are muitple levels and bosses inspired by nintendo franchises. Like for example, instead of Metal Man stage. Its Mario Man stage. Its a mushroom kingdom stage and the boss is called Plumber Man. Or a stage called Xeno Man stage and its like a xenoblade CHronicles kind of level, and all the music should be in the style of Mega Man X. YOU WILL KNOW OUR NAMES MEGA MAN X REMIX. PLEASE

I wonder more for what 3rd party games they could fund for, but on-topic one i would like isn't necessarily one that needs to be funded but a Tales Of game. Tales Of has always spread through all platforms and Wii U neeeeds one T-T

stargate worlds

gothic 4/5

Final Fantasy Tactics A3! :p