Why does iTunes even have a setting that deletes your music when you click Sync? Automatically.
Syncing is a process of ensuring that two (or more) devices have the same files on them.
You remove them from your library, they'll be removed from your iPod. You remove a synced playlist from your iTunes, it'll be removed from your iPod. What's wrong with this?
Why does it download deleted apps that aren't even on your device? Automatically.
Go to iTunes preferences/Store and turn off automatic downloads.
Why can it sync through Wi-fi only when it is plugged in? This one just flat out doesn't make sense.
You can always wirelessly sync your iPod touch, iPhone, iPad by selecting it in iTunes and hitting sync. Or by going to the appropriate place on your iOS settings app and hitting sync there. No need to be plugged in.
It'll wirelessly sync overnight when it's charging, connected to the same network as your computer and your computer is turned on.
Why does it rearrange your apps?
It doesn't for me. When does it do this for you?
Many people don't. The alternative I suppose would be a drag and drop music folder, which would be impossible to keep organised, and be limited to music. Not sure how you would implement all the other synchronisation features that iTunes has via a drag and drop system.