I would have liked to see a more creative use of the controller, like Another Code did on the DS and Another Code R did on the Wii. They considered a lot more things when crafting their game, like the phyiscal attributes of the console or even how the system GUI overlays over the game GUI when pressing the menu button and integrated it into their puzzles.
In another code on DS for example you had puzzles where you had to nearly shut the device in order to make reflections of images shown on the bottom screen overlay with the images shown on the top screen in order to get a clue or in another instance, close the system completely (making it go to standby for a moment) to put a stamp on a piece of paper.
In another code R they used the system gui of the Wii that shows up when you press the menu button in a puzzle. If you opened the menu, it cut off the top half of symbols shown during a puzzle, which reveiled their true meaning. There were a lot of other examples in this game, but they only happened on certain occasions and mainly came into play during the opening of locked doors with certain security mechanisms. It's sad that the studio had to shut down at some point. I really liked their games.
ZombieU by Ubisoft made decent use the consoles features as well when you looked through crates. On the TV screen you saw your surrounding and had to look out for possible zombie attacks, while at the same time you had to manage your inventory on the controller screen.
On WiiU even combinations of different controllers like the WiiU Controller and the Wiimote could be explored.
Having said all of this however, I am aware, that such features would require the game to be optimized for one system (the WiiU in this case) and I am afraid, this won't be an option for Yooka-Laylee. If possible, I'd still very much like the game to make use of the controller in a more creative way than just "let's put the gui on the second screen" or "show the map and menus on the second screen". Perhaps improvements based on stuff that is there anyway might work?
Imagine there is a vision based skill, like having a dark level where Laylee used some sort of ultrasonic ability that makes outlines of the environments and enemies visible in a limited area of the screen. On other consoles all of it would happen on the same screen, but on WiiU you could use the the direction you're holding the gamepad to look around more freely? Or maybe influnce Yookas camouflage ability by drawing patterns on the touchscreen or whatever (if he even has one, but hey, he is a chameleon)? I'm just making these up and can't tell if this is something easy enough to create or not, but I think it'd be worth considering at least.