Get rid of BIOS. It's been around since the beginning and has been tweaked but still remains largely the same as it was in 1980.
http://en.wikipedia.org/wiki/Extensible_Firmware_Interface is the way to go. I know that you arent in charge of it but working with them might help it get adopted faster
Stop supporting PS/2 ports and put 10 usb ports on the back with ONE front usb header (not 3 like on the current P55 boards)
Jumperfree config. Or at least short jumpers so you dont bend a critical jumper because it's near the corner of the board and you hit it with your atx power plug and now the board is b0rked.
Move the atx power plug to the top of the board so its in the most convenient place and closest to the power supply.
Add a little space between the cpu/ram slots and the top Pci-e slot. Its a pain in the ass having to take out the top video card to get to the ram slots to install more ram. This could be accomplished by moving the cpu socket and ram slots up 1/8"
Leave a pci slot at the bottom so I dont have to put my sound blaster or some other card between my video cards.
Design a new mobo spec that fits in the atx cases but isnt a stock atx mobo (sort of like extended atx) so you can have board above where the back plate items are and wider than the standard atx specs. a bigger board is going to be required if you want to cram all this new stuff like multiple pci-e 16x slots, multiple pci-e 1x slots, multiple Pci slots, multiple ram slots, a southbridge, a butt load of sata ports, onboard audio, onboard network, onboard raid and of course power connectors on there. Adding an extra couple of inches to the width of the board and an extra inch or even 1/2" to the top would fix quite a few of these problems...
Possibly move the sata connectors up and the CPU down to where the sata connectors are now. Then you could have the pci-e slots connect to the southbridge which would sit between the slots and the cpu. That would also move the cpu to right next to the front intake fan where the air is the coolest. That would also allow you to rotate the ram 90deg and put it where the cpu is currently which would allow the power connectors to be moved up to the top and out of the way of the rest of the system.
More robust info on the power consumption, temps, and fan speeds, available via a software program that comes with the board.
I posted a second post later on with a link to a pic I did in MSpaint of a rough layout concept. It even has room to put an SSD ON the motherboard... yes ON as in directly connected to the board (not integrated, attached, sort of like ram is with a clip on the far end and the sata connectors on the other).
The first version could be via standard sata connectors but subsequent versions could be a specially designed interconnect that would eliminate the need for sata (a limiting factor soon) entirely and write directly from the cpu through the southbridge and to the memory chips on the drive. The best part is it will use off the shelf SSD's so you not only get to make a kick a$$ motherboard with the ability to attach an ssd then take it out and upgrade later if you want... but you also get to effect change to the entire PC market in the form of first adopting the onboard ssd connection then by dropping sata for SSD's entirely! You could be responsible for DDR3 like performance in SSDs! Plus because SSDs dont generate a lot of heat, are 2.5"x3.9", and made of ram chips so they are very light (about 95grams), they can easily fit on my layout design and not heat up or weigh down the system.