Makes zero sense that we have to buy more basic boards missing some features we might otherwise use because we explicitly do not want Wifi.
Like I don't need an integrated sound card. I get it it's part of all motherboards today. But remember when it was an and also and everyone that gamed was getting add in boards from vendors like Soundblaster, and Turtle Beach, and Roland? Now most people get by with whatever.
You know what... here's what I want in a motherboard.
Support for the socket of CPU of your choice. Be it AMD or Intel.
6 or more on board USB ports and expansion ports for another 4. All at the current high speed. Maybe one pair on USB 2.0.
On board high speed ethernet. Be that 10g or 5g as long as it can step down to 1g I'll be fine but I want it to support greater speeds.
Minimum of 2 high speed PCIE M.2 slots.
2 x16 PCIE card slots and 2+ PCIE standalone spots spaced so all can be used even if double height cards are installed.
Maximum slots for CPU support be they dual channel or quad channel and far enough that I don't have to dance to install a CPU heat sync. (Heck I could be ok with them being on the back of the board if my case supported it, if that means I gain a nanosecond or two of speed.)
Oh and a thunderbolt port. I want that as well for people that do multi-media work!
On board sound because everyone has it.
Actively or good passively cooled VRM's and other heat generating components.
That's it. I don't want your wifi, or your bling, or any of that stuff.
I'm from the era of beige towers when an aluminum Lan-Li case was AMAZING. I don't want/or need your bling....
Not saying I don't have LEd ram, LED heatsync, giant led intake fan on the side panel of my case and two Led intake fans on the front... but they were all bought for their function not their looks.
And this is why you aren't allowed to design motherboards.
A lot of what you want is already done, isn't technically possible and some of it makes no sense. Let's go through it.
CPU
Socket choices are based on the chipset and physical socket used. You don't get a choice as your choice fundamentally changes everything else. I'm not sure why you mentioned this at all.
USB
6 USB ports and 4 via headers is insufficient. My MEG X570 GODLIKE doesn't even have enough ports on the rear I/O for me. I have to use a hub via my monitor to get what I need plugged in. All I'm running are keyboard, mouse, headphones (charging), Bluetooth wireless headphone reciever, monitor hub, XBOX One wireless receiver, and a USB 3.1 type C plug for my cell phone to charge from. Without the ports on my monitor, I couldn't connect everything. I'm at least one port shy on the back panel. Lower end boards are even more restricted.
Networking
Onboard Ethernet is, was, and will be there for the foreseeable future. A lot of it is still 1GbE, but 2.5GbE, 5GbE and even 10GbE isn't unheard of. It again depends largely on price point and market position. Workstations boards get your 10GbE, but options like MSI MEG X570 GODLIKE get a 2.5GbE port onboard, a single 1GbE LAN controller and a 10GbE add in card that can step down to lower speeds. Several Z390 and X570 motherboards with dual LAN have 1GbE and 2.5GbE ports on them with some even going to 5GbE.
The funny thing is, like onboard audio, we sort of expect every motherboard to have integrated networking. At one point, we used to bitch about it because onboard network controllers were trash compared to add in boards from Intel or 3Com. The funny thing is, onboard network adapters are still pretty awful compared to their add-in board counterparts. Although, you can get i211-AT's and controllers like that in add-in board form. Again, they are bottom of the barrel but the expectation is that these controllers are present. Most people springing for an add-in board will buy something a bit nicer than that. I've got an old Intel X540 converged network controller. It's a basic model, but it runs circles around integrated options like the i219v or i211-AT. Stuff like that is what you buy when you really want to move data.
NVMe/M.2 Slots
You do get two M.2 slots on most motherboards. There are some really cheap options that give you only a single one, but even the X570 Gaming X gives you two. I see a ton of boards with three slots or sometimes more. This also isn't really needed as you can adapt these to work via expansion cards. Furthermore, M.2 is an awful form factor for desktops and to make them work on motherboards makes their layouts worse.
Expansion Slots
I'm not totally sure what you mean on slots. Most boards that support dual-GPU's, space them out so you can use double height cards without issue. As for additional slots, that varies a lot. You usually get at least two usable PCIe x1 slots though. You can get a more usable configuration for expansion, but it often requires stepping up to HEDT to get a high enough lane count to give you two additional x4, x8 or x16 slots. Some limitations are simply due to the size of today's GPU's and the limitations of the ATX form factor itself. Solving those issues is a bigger discussion.
Memory Slots
You do realize that most motherboards do in fact, support the maximum number of memory slots a given CPU can handle right? You could increase the count to six slots for mainstream motherboards if you were using single-ranked DIMMs or something, but it's not really beneficial. The boards that stick with two DIMMs or four DIMM slots in the case of some HEDT boards trade expansion capability for increased memory clocks. It's that simple. If you want to run DDR4 5133MHz modules, you aren't doing it in a 4xDIMM configuration. You sure as hell aren't doing it with 4, dual-ranked 32GB DIMMs or some **** like that. That's why the ASUS Maximus XI APEX has only two DIMM slots. It will break DDR4 4000MHz speeds with ease.
You made mention of being able to use your RAM slots without worrying about heat sink clearance issues. This is what I meant when I said what you were asking for what's possible from a technical standpoint. The reality is, signal degradation occurs when the modules are further out than they are now. They have to be close to the memory controller. We could have slots further away from the CPU when the IMC was part of the chipset and we were talking about SDRAM, DDR1, etc. which all operated at low frequencies compared to today's modules. Motherboard makers have to design their trace layouts with care to avoid signaling issues at the distances they use now. So, there isn't anything they can do about this now. It's why I don't hammer them on this problem in reviews. It's up to Intel and AMD to fix, not motherboard makers.
Thunderbolt
I agree, but at the same time its out there on motherboards suited to professional work. Gamers don't need it. Thanks to Intel and others who helped develop the standard, big royalties are involved in using it. Most motherboards don't integrate it as it increases costs. Until recently, it was pretty much an Intel only option as well.
Onboard Audio
Accepting Integrated audio is kind of a weird thing to do as I'll illustrate in a moment. Yes, you need sound, and in my opinion, if its good onboard audio great. I'm happy to have it and not waste an expansion slot or deal with some external crap hanging off the back of my machine. However, cheap onboard audio like the CODEC used by the X570 Gaming X, I'd rather not have at all personally. The only bonus is that its so cheap that it really doesn't impact the cost of the board a whole lot. It's like the cost of a fortune cookie with your Chinese take out. Sure, it technically costs something, but it's given away essentially for free because it's costs are factored in with everything else. It's also customary, and therefore accepted that you will get some sort of onboard audio with every board.
Back in the early days of ATX motherboards, guys like me were livid that they had to pay for ****ty audio we wouldn't actually use. The old AC97 audio was absolute **** and early on, I wouldn't buy a motherboard that had it. Eventually, I had no choice as every single motherboard on the planet ended up with onboard audio.
Onboard WiFi
I'd like to point out that you basically accept audio as something you just have to deal with even though, people use to make the same arguments against it that they use against onboard WiFi now. External DACs and proper sound cards are still way better than integrated audio usually is. When you have integrated audio on the level of a proper sound card, you end up paying almost as much for the board as you would for a similar board with an external sound card. That is, to get the same VRM's and other features plus add the sound card, you'd end up paying as much as that ultra high end motherboard with good audio.
The thing is, you need sound so people deal with it and go with a DAC or add in sound card if they feel like the onboard audio isn't good enough. These days, we can make the same argument for WiFi. You need online connectivity. Right or wrong, many people just opt for WiFi because its easier than running cables as far as they are concerned or because doing so is prohibited by their rental agreement, or other people in the house won't go for it or whatever. Or, it's expensive to do properly or the user can't do it themselves for whatever reason. Manufacturers include it because it's more and more of a necessary feature and it's super cheap to integrate. The people who don't use it are just like the audiophiles who ignore the onboard audio they've paid for and opted to install an add-in board or external DAC.
In a perfect world, I agree with you and it really shouldn't be integrated into high end motherboards so often. Having said that, it costs nothing and it's not hard to disable in UEFI. One day, I expect it will be so ubiquitous we won't talk about it anymore beyond the integrated controller being good or bad.
VRM
Good VRM's are what you get at the higher price points. Sorry, but VRM implementation is one of the most expensive parts of the motherboard. Going cheap is what gets done to bring the prices down. Or, if your some companies, you do this on higher end boards and lie about doing it and hope guys like me don't notice and call you out on it. As for cooling, active or passive, I don't care so long as it get the job done. Most VRM solutions are cooled adequately. Believe it or not, you could take the VRM heat sinks off in some builds and be perfectly fine.
Bling
<Insert OK Boomer Meme> I too come from the Age of Beige PC's. While I can understand why some people get mad about RGB LED's and fancy heat sinks, or whatever. The general argument is: "I don't want to pay for something I don't care about and wouldn't use." I get that. I really do, but frankly, RGB LED's are super cheap. The X570 Gaming and Gaming X are $10 apart and onboard RGB LED lighting is the difference. The X570 Unify from MSI is $250, a full $100 more than the X570 Gaming X from GIGABYTE and it features no onboard RGB LED lighting. It's pretty cheap to implement and you can turn it off if you don't like it. You really aren't paying for it in the active sense. It's like your onboard audio. It's so cheap, its practically free.