It is common knowledge that the 500Es wiring harnesses and a/c blowers go, among other annoying parts... But the 500E is amazingly solid and well put together, perhaps better than a newer E55.
The E55 would seem the better fit in terms of the warranty, technology and creature comforts without the FU, look at my bulging fenders. Faster too, but not by much.
Tough decision for sure... but as said before...you probably can't go wrong or be unhappy with either one.
I also was looking at C36s and C43s a few years back and then decided on the 500E. The E55s were still way high in price at the time and besides the big AMG rims, the looks didn't really move me like the 500E did.