The "Desk" menu application switcher seems to have been added in 3. You're probably right that 2 is closer to 1; I half wouldn't be surprised if the only real difference were the changes needed to remove the Twiggy drivers and add the Sony driver.
Somewhat related, but one time in a different community someone told me a story about how one day they were browsing eBay, found a couple of ex-Apple ProFiles, and then didn't bid on them for one reason or another and now they're kicking themselves because "they probably had the lost Lisa Office System 4 source code on them." Is anyone aware of any plans to make an Office System 4 before things ultimately turned towards Macintosh/MacWorks?