My pixel art workflow is kind of weird. I make backgrounds/tiles/decoration art with GIMP, but items/characters/animations with aseprite. I make low-poly 3D models with wings3D, I won't/can't really do hi-poly.
I like the freedom coding in PyGame with no engine gives you, but nowadays I also make games in HaxeFlixel. I can add python libraries like MoviePy and create small video clips and tweet them right from inside the game. Distributing a game with PyGame and native dependencies is a pain though.
I have discovered the Yarn dialog editor. That is pretty good.