You see, not everyone will use their PCIe x16 slot for a dual slot graphics card. They might use a single slot one. Or they even might use that slot for something else, like a professional hard drive controller. Not everyone is going to be using those for graphics.
Also, it looks good on paper. When you compare products between different manufacturers, they can claim they support more slots, so they can address a bigger audience and maximise potential sales.
Could they come with a "better" design, where the x1 slot sits further away? Possibly. Is it worth doing though? Probably not. To redesign a motherboard, even to that small stage, it would cost them more money, rather than to slop on and populate as much of the board as possible with features.
oh so its mostly marketing fluff, you think... thats annoying. They could make a cheaper board by not bothering with some of those connectors. I guess this way it also works for the largest population (ie those that have 1-slot GPUs).
What are these hard-drive controllers you speak of? you mean those PCI-E raid SSDs?
The simple answer it entirely depends upon YOUR use. At Home I can rationalize a MOBO/CPU that doesn't support 4-WAY SLI is a waste to produce, but at the Office a MOBO with anything less than 4-WAY CPU's (4xCPU's) and 32xDIMM slots is a waste to produce.
Not everyone needs a discrete CPU and many of those folks need a huge permutation of PCIe (including PCI) slots in various bandwidth and placements.
I'm looking for a H/z77 matx mobo with 1 Gpu slot, 1sound card Pci slot and one of those shorty pcie slots but nearly all mobos have umpteen gpu slots and one or the other , but not one of each of the other slots. Found a nice Asrock ATX with what I want but would then have to spend more getting an atx case - come manufacturers - we dont all want multi GPU slots - but I cant be the only one wanting to to cater for different cards