I can identify with onboard audio not being the greatest and wanting to use a discrete solution. However, the rest of your rant is not very good. Many newer motherboards like my abit KN8-SLi already lack serial and parallel ports. If you don't want the ports, get a board that lacks them. Ditto with integrated video and SLi/CF. SLi/CF is not that expensive and there are chipsets that don't support it (NF Ultra series and Intel 945/965.) Running two GPUs SLi or CF is usually dumb, but the boards themselves are great. The advantage of the SLi boards are that they have two high-bandwidth PCIe slots, either as 2 x8 signal/x16 slots or 2 x16 signal and slots as opposed to the non-SLi/CF boards having one PCie x16 and one or two PCIe x1 slots. I run my single GPU in one slot and a PCIe x4 SATA disk controller in another. Very few motherboards have a PCIe x16 slot and a PCIe x4 slot, or they put one lane to the x4 slot, which will bottleneck any SATA card with 4 or more drives attached.
I can take or leave FireWire as I've never used it either. Intel decided to drop PATA support from the 965 chipset, so it would be possible to get an IDE-less 965 board. However, most optical drives are PATA and judging from the feedback here, lots and lots of people use it. Floppies are outdated except to flash the BIOS with. If the vendors would ship CD ISO images instead of floppy disk images to flash the BIOS with, then the floppy could die. Otherwise, you need a floppy to flash the BIOS. There are some Windows-based utilities to flash the BIOS with, but I neither trust those utilities nor run Windows, so I put a floppy in my box just to flash the BIOS (it has a USB card reader, too.) On-board NICs are generally quite good as they are gigabit and connected to the chipset via PCI Express. That is much better than 99% of discrete NICs out there, half of which are 10/100 and not gigabit and almost all of which run on the legacy PCI bus instead of PCIe.
I suppose you don't include SATA and USB controllers, fan headers, and PCI slots in your "everything else" category? USB and SATA can be handled by discrete cards and generally SATA on a discrete card is better than motherboard SATA as the motherboard SATA controllers bottleneck if you run a RAID on them while discrete cards don't. Only the ICH8 (Intel 965) USB controller can throughput full bandwidth to two I/O-hogging devices on two different controllers- the rest seem to share bandwidth among all devices on all controllers. Discrete USB controller cards don't seem to have this same problem, else you could just plop in another card and it will be solved. PCI is also at least as legacy as PATA is and yet you don't call for its removal either. Odd.
I personally don't mind having some "extra" stuff on my board as there are not nearly enough slots to add in all of the discrete cards to handle everything that's integrated into a motherboard today. It's also a ton cheaper to put it on the board than on discrete cards. Also, if you don't want to use an integrated part, then you're free to use discrete cards for that function. Thus I really don't see much of the trouble you are.