The 2 things I noted were: no 64 bit slots, nor PCIX slots on the non-sever 64 bit CPU motherboards so the IO can be 64bit. If there's a wide path on the CPU, why not on the rest.
Also, all the fancy cooling could be larger and cheaper, if the AGP cards were made with the heat producing parts on the other side of the card, where there is more room. Unless there are some serious RFI issues, this should have been done at least 3 interations ago. IMHO