M5 positives: great viewfinder (no RF patch flare), shutter speeds viewable in VF, spot metering, vertical strap lugs (to me anyway -- it could be a pain if you carry two cameras on straps), last of the hand-made measure-and-adjust M's.
M5 negatives: no mercury batteries available (may need conversion), no winder/motor accessories, heavier than M6, larger than M6, meter needle drifts a little if camera not held level (minor annoyance, easy to adjust to), legacy system (cameras are generally older than M6's), age, parts availability (?), issues with some lenses (including collapsible lenses) due to meter arm in the light-path.
M6 positives: smaller, lighter, winders/motors available, solid state electronics, batteries readily available, parts readily available, age, usable with all Leica lenses including collapsibles and those with "eyes".
M6 negatives: RF patch flare, in my experience Leica's electronics not top-in-class (although many experience no problems), some find rotational direction of the shutter speed dial annoying (never bothered me), rumored rf-allignment issues (not a problem on my sample).
I have both cameras and enjoy them both. I like Tom Abramson's rapid winders and so am glad to be able to use them on the M6 when needed. I know some don't like the look of the M5; personally, I think it is a great-looking camera and a sleeper in terms of its feature set.
No bad choices here really. Good luck.
Ben Marks