There's nothing wrong with using MS Paint. It's how you use it.
I pair it with video editing software OpenShot to allow images to move, attach transparency, and change its colour. It also helps to use colours that aren't part of the default MS Paint palette.
Mikoma
I suggest that you check this page out:
NG Wiki > Creator Resources > Animation Resources
(https://www.newgrounds.com/wiki/creator-resources/animation-resources)
There's a lot of software here that can be used for animation, some of it is paid while others are free. Maybe you can find something here that you would want to use. I would recommend trying out Krita, since they recently added animation features and it might be worth checking it out.