If you have a folder-based project, you can just copy-paste directly over the files in the animation folders. Is it really that much trouble? I'm not sure I'm clear on why this is so tedious. You can do the same for audio - just copy and paste files over the ones in the project folder to replace them.
Also no matter what folder structure we choose, I'm sure there will always be other tools out there using different structures. I'm not sure what a good way to solve this in general is, other than making it easy to reimport a whole animation at a time, which should already be possible either by reloading from disk or importing spritesheets.
The original post also references "many oversights and problems" without addressing any other than re-importing animations. If you actually listed them I could perhaps address them by adding new features, but without that there is nothing I can do about your complaint.