I'm thinking the solution here would take some major development. The app would have to stop the driver for the current iPod from being installed and instead present a driver for the older device you want to emulate. Most likely your current device running the app would probably have to be jailbroke. It would also take some testing and playing around to make sure the driver worked with the current device.
Before going as far as creating an app or something you could try playing around with different drivers on your own system while having your current device connected. Just go into Device Manager, find your device, right click and update driver. Then try to manually add the driver of a shuffle or something. See what works. Then decide if it is worthwhile to pursue.
I have an alternative take on this problem:
I have just bought a Classic 160 Gb at Amazon few weeks ago and I have been facing the same issues as you.
I do not use Mac OS X, nor iTunes to sync. I run Linux and I use Media Monkey on a Windows VirtualBox Machine.
During the past two weeks I have tried everything that I could find. iTunes have not even been able to read my entire collection (strange, right?)
My findings
I have just restored the iPod firmware a few minutes ago. Started MediaMonkey and sync'd 10 songs from an ordinary random artist. Disconnected and the songs were there, nice. So the iPod is actually working. So far, so good, I have figured that out before.
However, in the meantime, while I was checking my library, I recalled that I have some songs from Japanese bands with Japanese characters in their names. Historically, this would be very error prone. So I did gave it a try, and sync'd 64 songs from that band. Disconnected the iPod and the songs were all gone.
So apparently the 2.0.4 firmware does not handle these characters very well. Check your library, make smaller tests. I am about to restore the iPod again and will try to sync some more files with normal ASCII characters. Will update you.
My old, now dead (waiting for a new disk), iPod, running 1.0.2 was able to hold those files nicely.
Best Answer
You could try using Rockbox, however you might want to check whether or not your iPod is supported. Rockbox is an alternative firmware for your iPod classic that allows you to copy music files just like a normal MP3 player.
http://www.rockbox.org/wiki/IpodFAQ
It even plays Doom!