Yeah, exactly. The other big factor is that the lines are vector but the flood fills are pixel-based, so accuracy depends very much on the width of the lines---

Yeah, exactly. The other big factor is that the lines are vector but the flood fills are pixel-based, so accuracy depends very much on the width of the lines---and even the rasterization algorithm used for the lines. Add to this the issue you brought up about thick pixelated lines making many fills redundant, and you have a pretty good idea about why automated upscaling of these games will never be very satisfying. Also, the sprites in the games are not vector art, and the games depend on the sprites covering exact areas of the background imagery.