i've been doing MC and iPod for over a year now and have never had any major problems. there are times when i'm sure itunes would be easier if you dont want to worry about it. and whenever apple releases new features for the iPod there is a delay beofre it is working with MC because they have to reverse engineer everything to make it work.
itunes is a solid program, but with hardly any customization available and very weak tagging tools. but if you want to use your music like apple wants you to, it does it well.
MC on the other hand will adapt to however you like to listen to and organize your music, has very good tagging tools, very good smartlists, and a big feature for me (having 2 iPods in the house) is that you can have multiple libraries, so each user can have all their own music, playlists, ratings, etc.
so i guess what im saying is i much prefer MC, and have got several ipodding friends to agree as well, but i see why some people who aren't concerned about the more advanced tools, would use itunes. thats my 2 cents.