Battery issues
 

I have owned my 2004 E500 for three years, and I have had to replace the main battery three times (auxillary battery replaced once). On two of those occasions, the battery issue happened soon after being serviced (one day or so), and the dealership (very reputable) says the battery is dead and needs to be replaced. They are not sure why the car goes through batteries this quickly, but they cannot prove it is the alternator. The last battery had been replaced 2 years and 3 weeks ago, so it was three weeks past warranty. It seems odd that the battery seemed to be fine between service appointments (10 months) and started to have issues just after the last service.

Any similar issues and/or feedback?

it is not acceptable that the dealer 'cannot prove it was the alternator'. this is a basic test.
Mercedes late models are notorious for suffering from parasitic drain due to the high
number of electrical and electronica appliances. it is not uncommon for a module of some
sort to remain 'on', thus drawing current even when the ignition is off.

systematic testing of devices should be made using amp meter on battery.

Battery/ALT
 

I had the same issue with the Aux battery. The dealer found an aftermarket battery in our 2003 E500 and claimed that was the reason why we were getting malfunctions. 24 hours After replacing the AUX battery with a MB factory battery, we received another critical malfunction (red lights, stop the car immediately message). Once we took it back to the dealer I demanded that they rediagnose. The dealer found out that it was the ALT and replaced it under my warranty.
I suggest you ask the dealer to look at the Alternator...

Thanks for the feedback. I had issues with the Auxillary battery and main battery a couple of years ago. They replaced both, and they indicated that since they could not prove it was the alternator, the extended warranty would not cover. I had no issues until a couple of weeks ago - with the main battery. They did perform diagnostics and noted no significant draw on the battery.

E500,
along with ALT. possib. bad , one or more control modules might not be going to sleep or could be even be wakeing up over night . at my shop we have a device that plugs in to OBD connection and device over night will tell you if one or more modules are not going to sleep and draining battery . would ask dealer to do the same, main batteries last along time in a MB. most over 4 years up 7 years because they are out of the eliments in the trunk . now aux battery do not last long they are only tractor batteries !!!

Jerry