The user interface between Apple and Android is very different, and people get used to one or the other and changing can be hard.
That said, Android functionality is far, far more flexible.
On your issue, I think you use playlists. Put all the music you want on the iPod into the iPod playlist and stuff for the iPhone in the iPhone playlist.
Then sync just the playlist required for the device concerned.
But like I said, it's been a while and I am certainly no expert.
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