Date registered: Oct 2009
Vehicle: 2003 Lincoln LS V8
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Even if you have a friend to help you do the labor, you should still consider the price of parts. The S-Class has a lot of uncommon and complicated systems, and parts can be very expensive.
Another consideration is insurance. You can call your insurance agent to get a quote on both cars to see if there's a difference.
Finally, if you're concerned with ride comfort, try to drive as many of the different suspension options as possible. S-Class comes with either Airmatic or ABC (hydraulic), and the E-Class comes with either standard springs or Airmatic.
Since you want to stay less than $16k, I recommend avoiding ABC. It's far too expensive to repair, and it's normally found on the higher models (V12's and AMG's) which are out of your price range. I'm not too familiar with Airmatic, but you can check the E-Class forums to see what typical repair costs are.