I have been using an external Hard drive since I bought the Wii U. However, I realised that I have only used not more than 50 GB on it as I prefer a physical copy

I really want to get rid of the external hard drive as it takes up some shelf space and one extra power cord to use it. Based on some research i found online, ppl said that micro sd cards cannot be used to store wii u game. What is some other good method I can use without the needs of a power cord? 

2.5" HDD

I never needed more than the 32gb that came with it since I bought mostly physical games, but you could use a USB stick

I bought an external HDD pretty early on. I think it was 500gb and it got a lot of use. I bought several games, digitally.

Not sure what percentage I used but it was necessary in my case.

are there any limitations / disadvantage of using USB stick?

Use an External HDD and buy this Cable you won't need a power cable.
OEM UTStarcom USB Y Adapter Cable for HTC HD2 - YC150B https://www.amazon.com/dp/B002W8EDOM/ref=cm_sw_r_cp_apa_so9LybY1GRM18

Possibly, USB thumb drives are not designed to be constantly reading/writing/deleting files, so that could wear them out. Prehaps a usb SD card reader would be fine or a small external hard drive or solid state drive would be best.

I have a 750 GB external hard drive I used back in college, but had since upgraded to a 1 TB drive that didn't need a power cable, so the old hard drive was just sitting around. I have quite a few digital games, so it worked out nicely.

This looks good. Thanks!  will consider this if there are no other method. i prefer to swap it with a smaller device (thumb drive etc) if it is possible as the external hdd really takes up a lot of space on my shelf.

I just have the 8gb Wii U, and that's all I've used.