Load times are slightly faster. And in the Wingless version of Any%, animal grinding is simplified and faster as well. There's really no reason to use the Wii U version anymore unless you can't afford/don't want to buy the game on PC.

In the Wii U version, you would use the Legend of Zelda DLC Zone to grind for animals. Now, the grind is shorter and in Tropical Coast 1.

In essence, for the PC version: Make sure you have 100 animals by the end of Windy Hill 3. Complete Windy Hill 4. For Desert Ruins 4's requirement, you should get that normally while doing your run. Then when you get to Tropical Coast 1, stop proceeding when you reach this part of the level. Get the checkpoint if you didn't already, and... see those capsules? Open them all, then get KO'd by an enemy nearby, and repeat. You'll want to repeat this until you reach a little over 1000 animals. Complete the rest of the world, and your animal quota for the rest of the game will be fulfilled.