If this helps even in the remotest bit...
I'm now "officially" upgraded to itunes 11.1 (held out as long as I could, but finally upgraded to from 10.7 to 11.1... the latest as of about 3 weeks ago) and at the same time, I upgraded the ios to 7.1.4 (new apps require ios 7, ios 7 requires itunes 11.1.... grrrrrrrrr).... So that's my setup.
I have 80Gb of music and a 64Gb iphone (55Gb is dedicated for music).
I have managed over the years to create a number of smart playlists that funnel down to one or two playlists I dub my "radio station"...
One static playlist that is "permanently stored", comprises my core music (about half), and several other playlists that make up what I normally play.
I went in and said "only what I choose" and I only choose the key playlists (not all playlists, not one song, not one artist, not one genre, JUST the specific playlists). The end result is every time I sync, I end up swapping in and out about 20 songs a day, and I am reasonably satisfied the core songs I listen to will stay on my phone.
I also went in and said "do not check for new music/videos/tv shows/whatever you might want..... I'll keep it synced with itunes, thank you very much" in the settings (icloud, I think and music)
It seems to be stable since I upgraded, although the only real problem is the fact that it takes many long minutes to sync the phone every time, stuck at the "waiting for changes to be applied"....
For anybody who has similar problems as Anarion, you might want to create a smart playlist that is "type is music", manually sync your artists/playlists, and do what I did which is to only sync that playlist (and any other playlist you happen to be using)... I think part of that horrifically long sync time is the phone going through deleting songs off the phone that are not in the database.
I think what might be happening with the ever growing "other" category is this:
1) itunes goes through and identifies items in the database to remove (In the case of a playlist only sync mode like mine, it's a lot better at removing old items out of its database than if you say "go ahead, you can manage EVERYTHING and I'll poke at you from time to time with itunes".... That used to work well without the cloud (e.g. ios 6 and itunes 10.7), but now apple wants everybody to use their match and icloud service (and expects that's the only way people use it), so it probably is quite buggy there.... if you say, "no, no, I'll manage it through a playlist", it still makes sure the songs are nice and proper (as opposed to the phone going to the cloud to "sync" itself).
2) itunes then tells the phone to remove old items on the phone that are no longer in the database (this is where, in a perfect icloud world, the phone would just do on its own, but itunes mucked with its database). That's where the phone is now spending all its time looking for things that might need to be deleted.
3) when the phone is done, itunes then adds new entries in the database, and proceeds to copy over the new media.
4) sync is done.
If this is so, that could explain why "just sync everything" causes so many problems (maybe due to allowing ios 7 to "check the cloud for new purchases", etc).... If itunes and the ios are both screwing with the database, orphaned files might get created far too easily which would explain the "other" category.
Good luck to all.