I did this. Again, only at the PCB stage. The schematic was neat enough. Laying out the circuit to prototype on a breadboard worked ok, and once I had the code good, it all worked as expected. Then I went to draw a PCB for it. No matter how I tried arranging things, I had far too many lines trying to cross over one another to make a neat and orderly PCB. I realized in looking at what was happening, that if I changed the pin usage a bit on my micro, I could get clean shots from the pins to the pullups/component being controller/external connector. Bingo, much cleaner PCB layout, and all I had to do was change some initialization code at the beginning to swap the pins around.
I never felt a schematic should reflect any sort of physical layout of the circuit. Maybe that's the wrong way to go about it, but I use the schematic to display the logical connection of components in a neat and organized fashion. An input jack on the schematic may be on the left side of the sheet, but on the actual PCB maybe it's on the bottom, or the right side of the board. (ok, maybe not a great example, being in a left to right oriented country, I would tend to want the inputs to be on the left and outputs on the right of the actual PCB). Plus things get modularized in the schematic, not everything has 'wires' going to it, sometimes there are just tags. When it all fits on one page, I just put it on one page, but for something more complex, perhaps the power circuit would be on one page, the main processor and I/O on another, and output circuits on a third page. Just to keep it organized.