Pencil 2d is a simple program for animating cause of ots simple user interface, implementing some of this features aem sure will add complexity to the software. Like that layers mask or so can just overwhelm pencil users who are not used to those kind of terms or functions. What i suggest is to just add the lasso tool, shape tool,ruler blezier curve(optional) and a couple of extra brushes e.g, airbrush. I believe this tools will make it a program that fits standard and even reach top both in features and interface 
.although adding blending mode, mask… Isnt bad but i hope it doesnt make the program look complicated