The 1st one is related to auto-org.
The empty folders removal is a very good idea that can save time but sometimes it is not wanted (e.g. auto-org from several folders when you download files) so you should add a check box in the auto-org dialog.
The 2nd one is about sync with small capacities devices.
Let's take an example.
Monday: i prepare a sync list with 2 albums (one choosen from the location node and the other one from the artist node), i sync in order the tracks already stored are deleted and replaced by the ones i expect. i'm going to work and i'm happy to listen to that music
Tuesday: i want to change the albums stored on my player so i go back to the sync options and... i need to locate and un-check the previously selected albums: this is annoying when you own a large music collection as you must browse all the main branches/nodes to find them. The solution would be to only sync via (auto)playlists but needs several operations to prepare them.
So please, add a simple "Reset sync list" at the top of the sync dialog.
PS: don't know if this can be improved easily but when you add an album in your sync list, it is not marked in the other nodes (eg. if i choose 'Artist|Abba|Forever gold', it is not reflected as selected/checked under 'Albums|Forever gold (Abba)'...)