I think I have a workflow for animating pixel art and still use TVPaint for the animation.
I have TVPAINT 11 Pro and one of the options on exporting your animation is a sprite spreadsheet. The great thing about that is that PyxelEdit has a tile setup option, which is essentially a sprite spreadsheet. The tile setup can be used for making backgrounds or animations. All I have to do is import the TVPAINT sprite spreadsheet and I do the final artwork in PyxelEdit. BOOM, I am hopefully off to the races with creating this mobile game.
You have to celebrate these very small victories, I tell you.