I find that I never pick ingredients from plants anymore because I do not like how barren the world looks with nothing but the post-harvested plants in it. So is there any way to mod the game so that the plants keep their pre-harvest appearance after you harvest their ingredients? I have looked through the entries for the plants and mushrooms and only see a single option for the mesh each uses, rather than a before mesh and an after one. Is the change of appearance something in the mesh itself?

I believe the change is indeed defined in the nif. It marks part of the mesh seperately to be disabled when picked. Not sure how to prevent that though.

You would have to edit the meshes, and copy the 'full' plant to the 'empty' plant slots and delete the old empty plant slot.
I used this method when I made my tomato plants in the http://skyrim.nexusmods.com/mods/14152.

Thanks guys!