I would be a little surprised, but only because Barth et cie obviously don't feel constrained by camera-designing tradition; I think in Matthias' review he mentions approvingly that they made not the slightest effort to make this camera look like a 1954 Leica M3, and I like that too. So, I would guess they are equally unimpressed by the heritage of the 36x24mm image size defined by Alfred Huger Moses Jr. for his Simplex 35mm still camera of 1914 -- they aren't going to adopt that size unless there is a tangible benefit besides tradition.
However, if they could find a Moses-size sensor that met their other requirements, I'm sure it would fit in the body. If they also wanted to increase the pixel count (logical if they were to go to the bother of using a larger sensor) they probably also would have to go to a processor with more cores, and that would mean the need for more battery power and more heat dissipation; not easy problems, but likely solvable. The biggest reservation might be whether the cute little short-base, 0.67x range/viewfinder would provide the focusing accuracy people would expect from a high-megapixel camera. Redesigning that module would be a major project, and one might well ask whether the juice would be worth the squeeze...
Still (and here we are still very much in the realm of speculation) what interests me the most about the Pixii is that it is a software-defined camera -- other than the range/viewfinder, almost all of the "moving parts" are silicon -- and I would bet my bottom croissant that Monsieur Barth has written his software so it could be recompiled for a range of sensors and processors without too much effort. Who knows, maybe licensing deals might be in the future as well, opening up the possibility of interesting camera concepts in a variety of formats from various small-volume manufacturers...?