One difference might be that Krita existed as a project to write a raster graphics editor for years before deciding to double-down on painting, and did quite a bit of broad foundational work in that space, like aiming to operate colorspace-independently and implementing various general raster editing tools (e.g. a sophisticated layer and adjustment layer system). Krita retains those traits today, which I feel makes it broader in actual scope than MyPaint, which I think directly started out as a personal project to write a stylus-driven painting app and then grew out from there.