Blender also has a high learning curve but you typically don't need a PhD to understand the errors (instead you just watch youtube videos and copy what they do).

Removing faces from an STL and adding other objects is quite straightforward. Previously, Autodesk had Meshmixer and 123D, I guess Meshmixer is still available: https://meshmixer.org/ and I found it to be great for quick editing of the type you're describing.