I'm using 11.1.059 at the moment and currently can't really take advantage of the cover art support for a long transfer. I thought I'd take out a few songs that have a hot girl as an album cover and then sync them back, just to have some songs with cover art on them. This was just over 100 songs out of 2200+ total. When it was almost done, Windows locked up. The iPod database was fine and I could still browse and play all the files that weren't in that queue. But MC never seems to be able to open if the database doesn't get updated right. I tried deleting the folders, got another windows hang. After rebooting, I tried opening MC, thinking initializing is faster than deleting 2100+ songs (I had deleted the iTunes folder), but MC for some reason tried to rebuild the iPod database AUTOMATICALLY. I don't have auto-sync enabled, either. It froze immediately. Rebuilding never worked too well for me in any version of MC so I just don't use it.
Auto-initializing or auto-rebuilding, I'd prefer not to have these enabled by default. Maybe MC can be reworked to better handle corrupted or semi-corrupted databases with a pop-up dialogue box saying something like, "Media Center was previously unable to completely refresh the iPod database. Would you like to revert the database to the last good sync?" or maybe have options to rebuild database, initialize or revert to some sort of handheld backup that would delete all the files that aren't in the backup.
And I don't know if anything can be done about 4G/post 4G iPods needing to restart themselves before transfers, but maybe it's possible for MC to detect when this needs to be done to prevent lockups during uploads.