And this can only become a bigger issue since resolution increases while sensor size shrinks or stays the same. It is an old truism that you should care more about the quality of your lenses than your camera body, and that hasn't really changed.
The only problem is low light. My 600D takes fine photos in sunlight or with a flash, but otherwise the sensor noise is awful.
Seriously though, the comment about focusing on lenses instead of bodies is spot-on. Photography is the art of manipulating light, be that via off-camera flash, better lenses or picking the right time of day.
Getting a fancier camera body only lets you pick up the electrons that are already there, you'll see much larger improvements in your photo quality if you focus on the other things first.
Most wide-aperture lenses have larger AF motors to compensate with the exception of a few unique lenses that use a gear instead of servo motor(USM in canon parlance).
I would have said that the advantage in sensor size of 35mm DSLRs would give them a long-lasting advantage over anything with a smaller sensor, even with advances in that technology.
Sony's mirrorless camera is also more compact than SLR cameras with smaller (APS-C) sensors: http://camerasize.com/compare/#724,708
They're also quieter (no mirror slap) and having an electronic viewfinder allows you to see what will be recorded. For example, you can directly see the effect of a longer exposure or higher sensitivity.
The next important step for both companies will be the transition to mirrorless technology. As µFT and the Sony A7/A9 are showing, mirrorless is the next step in camera technology. It will be interesting to watch how Canon and Nikon approach this transition. As both companies currently make their money with SLRs, it is a risky step, but an inevitable one. If one of them missteps in that transition, it means at least a big set back if not a complete loss of their role in the camera market.