I don't really have any doubt, Oscar, that the larger sensor with the larger pixel pitch will have certain advantages, either in terms of wider dynamic range, less noise, a shallower DoF capability, or higher resolution if it has more pixels as well as larger pixels, as the 5D has compared with the 20D.
Since I own both a 20D and 5D, I could be testing some of these issues myself. Perhaps I'll get around to it, one day.
However, I feel there's one important issue that is often ignored when comparing different format cameras, and that's the DoF equivalence at a required shutter speed. It's widely recognised that small format cameras, particularly P&S digicams, are of little use for creative photography employing shallow DoF. But the reverse is equally true. They are of great use for getting good DoF at wide apertures and fast shutter speeds.
Most comparisons between a 20D and 5D, I can almost guarantee, will be at the same aperture, same ISO and very similar shutter speeds, almost as though DoF is never a consideration. Since both DoF and shutter speed are usually amongst the most important considerations when composing a shot, it seems to me appropriate to make comparisons between the 5D at f11 and ISO 1600 and the 20D at f6.3 and ISO 600, for example (and of course same FoV). DoF and shutter speed will be the same, but the 20D might actually have less noise on the same size prints despite having smaller and fewer pixels. I'd be surprised if the 20D displayed more noise in these circumstances, but it's something I'll have to check for myself I guess.