In a nutshell, MC's advantage over iTunes when it comes to the iPod is the same advantage that MC has in general -- incredible flexibilty and configurabilty. Not only is MC more suited to "unusual" situations such as managing 2 iPods on the same system, it offers multiple ways of doing such things. At first I used a series of Smartlists to manage two seperate iPod lists, but after a while it occured to me that the same functionality could more elegantly be realized by using custom fields and view schemes. I did not find iTunes this flexible for this sort of thing.
The thing about MC that impresses me is it can pretty much do whatever I can think of, and it can often do these things in more than one way. I'm always running into situations where I find myself asking "I wish it could do such and such" only to find out that it CAN do that. iTunes might have some advantages, but when I tried it I found myself constantly wanting to go back to MC. I considered iTunes when it came out, but it simply didn't have the flexibility and power of MC, and I ended up going back to MC.
I use MC to load Audible.com audiobooks on both my iPods and they work fine (just use the 147 build until the 150 or later build comes out.) The iPod will reflect the tag changes you make to aa files, and the Audible bookmarks are saved on the iPod until the file is actually deleted (i.e. you can continue to sync it without loosing your existing bookmarks.)
The only caveat with using MC and the iPod is with downloads from iTunes.com, but there is a workaround for this. You need to take a look in the "portable digital players" forum for details. The bottom line is that after using both programs, I prefer MC.
Larry