Lots of interesting points made. What I've gleaned from this is there isn't a super compelling performance reason to choose one over the other. Wet performance isn't all that important to me....I don't plan on riding in downpours, and when I did get caught in one I found that rain striking my face at anything above 10 mph was really unpleasant, and the wet braking performance with my rim brakes was adequate.
 
The reason I posed the question originally is that I'm undecided if the P38 is going to replace my commuter bike or my "go fast" bike. Micah at Easy Street suggested it could do both roles if I was willing to swap out wheels. Disc brakes would definitely simplify changing between the wide rim, heavy duty fat tire commuter wheel set and the skinny speed set. That convenience comes at a pretty high cost though...going to discs means I can't use any of my existing wheels, and the disc brakes are more expensive, especially if I go with the high end ones Vicki likes. It becomes a bit of a triple whammy if I start out with a frame set and build exactly what I want. Next to buying a used one, an "off the rack" bike is certainly the next affordable.  
 
I dunno what I'm going to do yet, but it sure is nice to have first world problems like this!

Aluminum rims made rim braking far more reliable, but flooding reduces that reliability.  The solution is to learn how to use your brakes in compromising situations.  It may take practice, in the rain or going through puddles.  Riding the brakes in the rain may sound counter productive, but before a steep descent it could provide some control you wouldn't have otherwise.

You don't see things like this happening with rim brakes:
 
http://www.nydailynews.com/news/national/trek-recalls-1-million-bikes-rider-para lyzed-article-1.2194234
 
For those with disc brakes, check your skewers.

Kool Stop duals is what I use on my bikes. They work great in the rain, mud, or dry. I use the mtb ones for my 26" and 20" wheels. They are Salmon on the front and black on the other end. The Salmon for wet and the black for dry. The Salmon end has a tapered sort of tip for removing mud and rain. $11 and free shipping with no tax from Amazon per pair. They stop both my Rans  V2 and Phantom very well in all conditions. Good luck on your choice.