Yeah, MongGrel -- definitely a case where some tech-George-Romero re-animated an old thread.
I've watched a handful of people over a dozen years decide what to do with computer cases that are filled with options. they think they have to use every ventilation hole, every opportunity to install another fan.
I'll choose a motherboard for certain features beginning with (of course) the chipset, certain BIOS features, and enough of the options that I can decide later if I need them. But I don't plan on "needing" to use an option if it wasn't in my original plan.
My Z68 boards all had onboard Asmedia USB3 and JMicron eSATA controllers. How many eSATA ports do I need? You need to them do maintenance, or at most connect to some hot-swap NAS or external drive box. I "need" at most one eSATA port, preferably accessible from the case-front. I "need" at most 1 or 2 USB2 ports -- accessible from the front. And I "need" at most 2 USB3 ports -- similarly accessible. I don't need a JMicron eSATA controller if I can run a cable from an onboard port to either a rear-backplate SATA-to-eSATA 2-port plate, or to a front-panel adapter similarly.
Also, the Z68's also had an Asmedia-Marvell onboard SATA 2-disk controller, which I wouldn't use unless some contingency required it (for instance, it would be good for those eSATA connections.)
With the new Z170 Sabertooth, I only get the onboard 19-pin USB3 controller. If I need more SATA drives than I have in onboard ports, I'll add a PCIE-x1 SATA 4-port controller -- nothing of a problem with 3 or 4 x1 slots on the board.
The biggest miscalculation I made with my Z170 build involved M.2 NVMe. I didn't figure on a major techno-lust coveting experience. Then I think I discovered the option of using the NVMe in a PCIE x4 slot with adapter card (~$20), which offers better NVMe performance. If the board-maker put an M.2 slot on the motherboard, do you think they'd "throw in" an adapter card? No, they don't and probably shouldn't. But I find limitations both ways: Can't use SATA 1 and 2 ports with the NVMe in the M.2 slot, because their bandwidth is shared as part of "SATA-Express" with the M.2. If I want to use the PCIE x4 port, I lose SATA ports 5 and 6.
These miscalculations haven't cost me anything, really. My Syba-Marvell PCIE x1 SATA controller is entirely available for external eSATA connection; my boot disk is on the onboard SATA 1, a second drive on SATA 2, and a hotswap bay in use is connected to SATA 3. I still have an onboard port available and useable -- connected to a second hotswap bay.
Anyway, I never use all the extras I get with my boards, and I accumulate that stuff -- much of which is still useful on a new board.
Maybe there are two different mindsets here, and I've had both of them at this time or that: You'd like to just slap together a PC after ordering the parts, fire it up and nothing more. Or, you could fancy you're a tech-guy for Dell, Origin or any OEM working in their testing lab, trying to build the ideal PC. You'd want an ideal number of fans -- not too many. You'd want a moderate set of front-panel options. You'd want just enough reliable SATA ports for more than one SSD or HDD. You'd want a case that gives you enough options for ventilation that you actually need to block some of them off to get optimal cooling and case pressurization.