Ok, so a lot of people are saying wifi connectivity and other extra add-ons... and some are saying they want the most basic board possible so they can add their own things without having clutter from unused integrated devices. I can see where both ideas come from.
I also think that the idea for one sata connector to be at the top of the board is a good idea, but given the workings of motherboards, that doesn't make sense from an engineering standpoint (I've also never had that many issues managing that ONE cable that comes down to connect a whole 8-10" from where the dvd drive mounts).
First and foremost, having the power usage of each device built into the BIOS would be awesome. that would make it very easy to see how much power your system is consuming on startup, and would allow users to extrapolate their load powers from there.
Second, and this may seem far-fetched, but you asked, I would like to see configurable PCE 2.0/ PCI / PCIe slots, meaning that you could rearrange the order of the slots on the motherboard so that you wouldn't have, say, 2 double-slot graphics cards (i.e. ATI 5850, 5870) in directly adjacent slots, which leads to both cards running hot since they can't get adequate cooling. Also, this would prevent other add-on cards such as tv-tuners or wifi cards from being in contact with a graphics card, which will also decrease the cooling to said card. Granted some people use all of their slots anyway, and this probably won't help those people, but for people like myself who have 2 add-on cards and a large graphics card (with plans to add another), configurable slots would be a great advantage. Again, this probably would be a challenge to engineer, but I think that you guys have some pretty smart people working for you.
Also, I've noticed that my ATI (or AMD now, i guess...) 5850 puts a lot of stress on the PCI 2.0 slot when my computer is standing. I haven't had anything fail, but it is disconcerting to see the slot bend slightly with that much weight on it. Somehow reinforcing that slot with an additional backplate that distributes the weight across the rest of the motherboard, or better yet, redistributes it to the case, would put my mind at ease.
Finally, an integrated SSD (that's ideally user-replaceable) would be AWESOME for installing the O/S. You could just dedicate SATA 1 to that SSD by default, and have SATA 0 available for the dvd drive.
That SSD would only really be useful in the ultra-high end boards, so it's not much of a reality for the mainstream boards. However, i think the other ideas, especially the configurable PCI slots would be VERY useful to the mainstream market.