Maybe I need to get higher quality mp3 but I got prodigy on cd and on usb and cd sounds way better. It is dead handy though, saves having loads of cds flying around.
Using my similar HUs I used USB all the time when I had a stick, but it recently died. You can obviously fit a lot more on a stick than a CD (or MP3 CD) enough for me to drive to Newcastle and back a few times without hearing the same tracks. The quality is just as good if you're using high quality rips and best of all no risk of skipping! I've had some of my mp3 discs in the glovebox that long that half the tracks don't quite play correctly with stuttering, complete skipping etc.
Consider 320kbps CBR or av. 256kbps VBR MP3s for WIN, I don't use anything less. Try ripping your Prodge CD with EAC and the latest lame and compare if you're still not certain.