Blitpaint is a sprite based painting tool (standalone exe for PC), you make sprites and you can plot them or paint them down to make nice scenes. I plan to export this plot data and images out so that you can simply read them in and create your scenes sort of dynamically :) (Created in Gamemaker 2.0)

It supports pixel shading, Pixel art mode, isometric mode, brushing with 3 drawing methods, brush dynamics and so much more, even supports pen pressure!

Give it a go!