First of all, thanks for this plugin, these features should be in WP core.
Anyway, now MLC is a bit limited in use, to make it really indispensable need to
1) add the possibility to sort for categories also in post popup, when add file to post
2) choice category when add file, not after, file per file
Also, could be useful to merge setting functions instead on a menu link, directly appending in Media settings.
In any case, great plugin, this could substitute the missed media folders organization
Thanks a lot