I must say, I had the exact same question.
It's been a while (read since MC16!) that I synced me iPod Classic 160GB with MC - I have simply been happy to listed to what was on the iPod in random order ever since. However, I have been adding stats such as star ratings on the iPod and music to the MC Library so I then decided to synch my iPod with MC18, but am facing this very same issue. I can't remember if this was the case years ago.
However, reading MerlinWerks comments re what I have set up to sync, it maybe that I have the sync incorrectly. I do like carrying the entire collection on the iPod (as it large enough to hold what I have), but I also like to listen to music that I haven't listed to either for a while or even (as according to the "Number of Play" in MC). I have several smart lists that list the music according to the number of plays, or that I haven't listed to in a while, but as said, I also like my entire collection on the iPod - just in case I facny a change. To this end, I has selected "All Audio", plus various different play and smart lists.
Is this incorrect?
I had thought that a list was simply that - a list of songs that I would want to listen to, not actually the songs themselves - hence I though that getting all music on the iPod with different list type would cover all scenarios. However, I am seeing the same issue as above.
I even tried to re-initialise the iPod, then sync, but as soon as the sync had finished, MC still wanted to re-synch the vast majority of the library. Apart from a handful of tracks. Lastly, I don't actually think that the playing stats or changes to star ratings sync back from the iPod to MC (and yes, i did have the "get playstats from the handheld on re-connect").
Edit - I have just read the WiKi page link to transferring files to/from a hand-held device, but it doesn't really say anything that I'm not already doing. In fact, I had set up the advanced option to "automatically remove all files on your device" during the sync - but all MC want to do is delete the majority of files it has just synced only to replace them with the same files!