Let's be very frank here, the E63 won and it will probably win in every comparison whether M likes it or not. Let's face it. The E63 is faster and better than the E55, so of course it is going to win. Not only that, when the M5 came out, we all knew that an upgraded E55 AMG (I may be mistaken, i am only assuming), could catch up, if not beat the M5.
I love the M5, but the naturally aspirated engines that are coming from the M division are limited in what they can do to out perform an animal that can just be forced induced. Either way, I would take the M5 over the E63, but only by a hair. The reason for this would simply be because of the SMG, and if the M5 came in 6 speed( like it does now in the US) then even more. I love spotiness and that is something that BMW has been able to accomplish.
Everyone is different, so driving the E63 may be what is right for guy A, but wrong for guy B. We all have our preferences and we all grew up driving differently. Some of us are lazy and just prefer an animal under the hood that is already tamed, others (like me

) prefer an animal under the hood that we need to tame and drive the hell out of (m5).
I think it is safe to say that many auto mags are going to pick the E63 over the M5, just because it has that little nitch.
Conclusion
The different between these two beasts is a matter of
degree, not a matter of one being better than the other.