Well, as a newcomer to the "open-sided case" market (not modded, the XaserIII comes with a window) I have to agree that the design of motherboards does not lend itself to looking pretty. Surely it would be sensible to allow a few more mm between PCI slots, and lay things out differently?
I suppose that we are too far down the "standardisation" road for it to happen - a new Mobo design would mean a new case to hold it. We'd have endless problems getting case and mobo to match.
As an aside, the Xaser case comes with SEVEN (count' em) fans as standard, plus a Rheobus. That is an awful lot of fairly ugly lookin' wires, and I've yet to figure out a way of making them look pretty through the window.
Of course I've had so many problems with this new PC that the window is something of an irrelevance. If I can ever get the side panel back on for long enough, I'm sure it will look lovely.