For those who want to measure the connector spacing on their A500 or A600, it is quite easy : use a flatbed scanner to scan the backside of your Amiga PCB and then a tool like Gimp to measure the spacing between connectors.
One can use a
caliper though to replicate the whole board scan+gimp might not be that bad.
How about this: Use or design some standard module to hold the FPGA(s) themselves, which connect to each such new Amiga replacement motherboard through the same connections of whatever kind it may be. Then each motherboard routes the FPGA pins as needed for that motherboard. Perhaps not all pins are used in each motherboard, such as pins for Zorro2 on A2000 are nothing on A500, but there are enough pins for A3000 or A4000 as well. Perhaps a couple FPGA modules are needed together to fill out enough pins to do everything if A3000/4000 CPU slot is present as well as Zorro and all other connectors. The motherboards get simpler this way, they basically hold connectors, routing between them, level shifting as necessary to the FPGA modules, and whatever PHY type stuff at the connectors. If you need more than one FPGA module, they are all the same thing, not different modules in different places. Each motherboard may have a different configuration to the FPGAs, but the modules don't need to get specialized for anything, for reducing engineering iterations/redundancy. If multiple ones are needed in a machine, some pins will connect them together in a suitable way as needed per motherboard.
Yeah some "dumb" baseboard module and standardized sized and slotted FPGA-boards to plugin would be useful. ITX is nice, but won't fit inside an A500, A600, A1200 etc.
And while you're at it, swap ISA slots for 3.3V (or universal if slots can be that way) PCI slots on A2000/3000/4000 and give them an active bridge to be useful.
Better keep to the specifications. ISA is 5 V in all cases, even thoe 3,3 V logic is accepted at input. Any FPGA must tolerate 5 V from ISA cards. And PCI is nice but it is timing tricky and I/O heavy.
Would you intend to have CPU slots present, or expect to use softcore 68K? CPU slot makes PowerUP board usage and OS4 Classic possible for machines that take them...
Softcore 68k is likely the convenient solution. But CPU slot is possible with FPGA provided you have the I/O connections.
Or, since we're reinventing things, why not turn A500s into A1200s, A2000s into A4000s, etc? Does that go beyond what you want to do, by leaving out people with broken A2000s now not being able to use their A2000 addons, and this is not what you want to do?
By loading the correct image you can downgrade at will.
And then go crazy, put MXM laptop graphics slots in the keyboard style computers, muxing their outputs with the "Amiga" graphics outputs like some Zorro gfx cards can do (PicassoIV for example), maybe laptop mini-PCI for wifi slot, internal SATA perhaps if chosen FGAs can do that, etc. 
This will likely increase cost in a non-benefitial way. Better to use plain junk PC for such uses.
What we really need is a proper production run of Amiga keyboards that plug into USB or ps2. This is of greater value for users of mini-mig or the proposed newer FPGA motherboards. I have a few A2000 keyboards with broken cpu's sitting in my cupboard! Its annoying.
Producing keyboards is really expensive. I know a larger organisation that did just that, the prices were in the parity of 800 USD/keyboard in larger series. Though maybe there are cheaper ways?, the pcb is cheap, the conductive rubber mat likely too. I think the real cost comes from precision molding many keys. the absolute cheapest is to modify existing keyboards.
Without some new standards how can we bring prices lower for interface hardware like wi-fi, usb or rj45? Amiga network cards and usb cards are getting harder and harder to source 
Dunno what you mean by "new standards". But these peripherals are easily created with a standard FPGA + standard interface chip if you need one. The catch is writing the Amiga driver.
Don't get me wrong I love my Amiga's but I would really love a new Amiga in a small tower with associated new keyboard and high precision mouse!
FPGA Arcade will do that for you already.
