The two biggest considerations for planning my next body are bulk and AF performance with both moving and low-lit subjects. I had heard that the 5DIII tracks moving subjects very well, but not that it's horribly slow in low light. The dpreview.com review of the 5DIII seems reasonably satisfied with its low light focusing speed and accuracy, though I understand it's just one opinion based off limited experience so it should be taken with a grain of salt.
If the 5DIII really has trouble in low light, that's a pretty serious blow against it, and would bias me strongly towards the cheaper and lighter option. Of course the number, utility, and coverage of the 6D's AF points can't compare to the 5DIII's, but speed in low light matters to me as well.
All that said, I'm coming from a 400D/XTi, which is one of the reasons I'm concerned about size and weight. Would any aspects of either of these autofocus systems seem like a step down compared to the Rebel? E.g. do the 6D's AF points actually cover a smaller portion of the frame compared to the Rebel's 9 points?
I think you may have misread my review (or I wasn't very clear). The 5D IIIs AF is excellent and fast in all situations - including low light. Very low light is obviously more of a challenge but mostly it locks fine. The 6D however has a slightly better centre point in near darkness - it locks a bit quicker and doesn't seem to hunt at all (yet).
I haven't used the 400D but the 6D focus points are reasonably well spread. For example in portrait format the top point is quite close to a person's eye if filling the frame with a face. In practice the focus points are well placed (for my use).