This is the only right answer.

I really really hope sunshine doesn't get remade. IMO It's easily the worst Mario game I ever played. 30 fps (although a remake could fix it), unimpressive power ups, only 8 major courses, and blue coins galore are horrible design choices. 

The game was really pretty though. 

Wii U - Twilight Princess
3DS - Paper Mario: TTYD

Wii u would be yoshis story

3ds would be Super Metroid

Wii U: Super Mario Sunshine
3DS: Super Metroid

I would go so far as to say it's among the very worst games I've ever played...

If they do indeed remake it, they need to add new contact to replace all the blue coins...

And they need to fix the ghastly pachinko level...

WiiU HD: Super Mario 64

No question about it, this already amazing game would now also look amazing on modern hardware. If they'd ask use the DS version's extra content, we'd have a winner.

For 3DS is a much harder pick. It already has a brilliant 3D remake in Ocarina of Time (and we got three in total even) and I would only want something that really benefits from the upgrade. Old 2D games are as such basically discounted because there wouldn't be much of a difference. Can I count Rare games when they were 1st party? I know it won't happen because even though the company was first party, the rights to their original characters remained out of Nintendo's hands. I would nominate Banjo-Kazooie. Otherwise, I'd take the following, because it's sequel released on 3DS proved how much the 3D effect added (still the best use of 3D in a game as far as I'm concerned) to the gameplay of this game.

3DS 3D: Luigi's Mansion

Mario Sunshine on 3DS could also work and it's something I can see happening in real life. Even though it's my least favorite 3D Mario, I surely wouldn't be opposed to giving it another chance. I'd take Zelda Twilight Princess on WiiU's successor; it's still too new and still playable on current hardware.

Man, I loved Luigi's Mansion. The atmosphere in that game and the visuals were almost perfect! And the gameplay was actually unique and something new from Nintendo. While I played, it reminded me at times of one of my all time favourite game: Maniac Mansion. Probably because of the side scrolling view and the fact that it was a mansion. xD But yeah, it was awesome, and I'd rather them make a HD remaster of it, improved with added gameplay and gamepad features, than to see it downgraded for the 3DS. But that's also due to the fact that I'm not much of a handheld gamer. =P

Eternal Darkness HD - 2nd party, but I've been waiting for a long time)
F-Zero 3D - the SNES original, Sega 3D remasters style.

For 3ds I'd like to see Mario Sunshine. I loved the exploration based 3d Marios more than any other platform game.

Kid Icarus uprising is my favorite Nintendo game of recent years (possibly my favorite game of the last 5 years) and I'd like it to get another shot at the attention it deserves so make that HD on Wii U... But perhps it wouldn't sell as you can pick it up cheaper on the more popular 3ds.

I can't choose....

This is so hard!

I can't just can't....

OK I'll try

Wii U HD Remake - The Legend of Zelda Collector's edition (All Amiibo compatible and fight ranking)
3DS 3D Remake - Super mario ALl Star plus Mario World (of course added features content Amiibo and Spotpass)