While I fully agree with you that the D100's standard sharpening in JPEG mode is lacking I think you'd likely find that you need to sharpen the images from any camera far more heavily for printing than you would for normal viewing.
Going back to Michael's original questions, I went from the D1 to the D100. The D1's autofocus is noticably better in its ability to 'lock on' to the subject quickly and accurately. I can't really comment on focussing speed since I'm using AF-S lenses which are equally fast in operation on both cameras.
In terms of processing speed, I shoot NEFs and to date haven't been held up by the D100 unless I use the compressed NEF mode which takes 40+ seconds to save each file.... However I've not used the camera for any sort of action photography to date.
My major issue with the D100 is that it seems to produce far more contrasty images than the D1, even with the tone compensation curve set to 'Less Contrast'. I find this a problem in that it's far too easy to blow out highlights or, if I try to compensate for this by underexposing somewhat, to loose shadow detail. On the plus side the camera suffers far less from noise than the D1, and what noise it does produce is random and 'film grain' like, rather than the horizontally banded noise of the D1. This means I can, if necessary, push the images that much harder.
On the subject of the D1x, I've always been a little uncomfortable with the idea of the 4028x1324 CCD meaning the vertical resolution has to be interpolated - despite the fact that this just doesn't seem to be an issue in real-world shots.