I'm looking to learn Shantae at some point and I see one PC time and the rest of them being Wii U. What are the main differences between the two and which one is ultimately faster?

As of right now PC is probably faster due to loads. PC loses a little bit of time to using items. other than that, they are identical.

If you go ahead and compare in-game time of runs done on pc to wiiu, the same as comparing wiiu to 3ds, you can see that pc 20-30 seconds faster, so as mamgar says, it basically depends on how fast you menu. Like unless you're very very slow at menuing, pc will be a bit faster.