There's a big difference between 1999 and 2000. The '99 is the old style s-class which was launched in '92. The 2000 style runs from '00-'06. Both are great cars, I prefer the '99 styling better, and I think the interior quality is better too. I don't see any reason to stay away from '99 as it is the last year of the w140 s-class and was probably perfected by then. There is probably a pretty big price difference as well.

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2002 Mercedes-Benz E320 4Matic
1995 Mercedes-Benz E320 Wagon
2005 Land Rover LR3 V8 SE
1999 Audi A8 4.2L quattro