You can use rhythmbox or several other things to manage mp3's, - rhythmbox also plays them directly, through the computer sound card and the digital connection. Think gtkpod, banshee and amarok offer various functionality, haven't looked in a couple of years (pretty happy with Rhythmbox, and got tired of multiple things trying to grab/manage the ipod when I plugged it in - so de-installed the ones I wasn't using).
iTunes is just a nightmare. My MP3 collection lives outside iTunes on a USB disk (with a backup on a RAID 10), so all I ever do is rip any new CD I buy, import the folder into iTunes, fix the art (and refuse to let it mess with them otherwise). And then either sync the ipod or add the mp3s directly.
Since I also have the same collection in Google Play Music, my Nexus (or any web browser) also has access to/plays all the songs the ipod physically holds - which seems like a good fall-back position
I still like/use the ipods as a dedicated music player (Alpine digital head unit in the car does a good job of driving it too), but iTunes is a horribly bloated, flakey and truly foul experience. Just wait until you have to re-plug, reset/reboot (computer and player) 5-6 times to get it to recognise it. Or even re-format and re-load the player. Bah.
In fact, when iTunes was all I used, it would seem to keep "discovering" albums I've had for years and add them to the ipod at the next sync. Which made me wonder if it actually had the music in the first place (hard to be really sure once you get over a few 1000 songs) - or was simply re-adding something it already had... Neither seemed ideal...