Are there any titles on one system that you wish were for the other instead?

Luigi's Mansion 2 should have been for the Wii U.

In terms of 3DS->Wii U: Bravely Default, Luigi's Mansion: Dark Moon, Kid Icarus: Uprising, maybe Kirby Triple Deluxe.
Wii U->3DS: Kirby & The Rainbow Curse aaaaand....that's pretty much it, lol.

Kid Icarus for U and 3D World for 3DS!

Love Plus for 3ds on the wiiU

Kid Icarus Uprising would've worked better on a console (especially with Wii pointer controls).

If I had to pick one, it would be Monster Hunter 4 moved over to Wii U.

Crossbuy for most of them. If I am able to buy VC games from GB and GBA and still enjoy them on the big screen, the same should be possible with all 3DS games.
The opposite has to wait for the NX!

I feel like Nintendo could've done what they did with Smash Bros and make a 3DS version of Mario Kart 8; however, one feature to add in would be the ability to play with both 3DS/Wii U players locally and online.

The Professor Layton Series on Wii U!!!!!!!! I love the art style they use in those cut scenes, so it would be nice on a bigger screen. Also the puzzles can be viewed on the big screen, where your friends can help you solve it.

And i agree with Luigi Mansion. On the game pad it can have like a first person view.

Edit: I also think Nintendo Land on the 3DS would be nice. With Local and Online multiplayer. And they can do like in Mario Chase, there can be like 2 players are mario, while 8 players are the catchers, then the map would also get bigger ( like in luigi mansion ) 

Pikmin 3 on 3ds is nice too. But the graphic quality would really go down. Wonderful 101 can also work.