These I am taking into account, except for perhaps an SD card slot, but I figured the good folks around here would probably just be more interested in what I'm using for hashing, and maybe what I'm using for control, and not so much the infrastructure chips that will make it all possible. The MCU in particular might get replaced with an AVR32 or an ARM device. I won't be running Linux on the MCU, whatever it ends up being, because that's too much overhead. However, given the board's specifications, I'll make sure that if people would like they can program the device with Linux, provided the resources to do so don't make the board cost anymore than it already would.
You make a good point. I'm just doing this because it interests me and not because I want to make money mining. However, I would be curious to know what the folks out there who are considering using an FPGA-based solution for mining would prefer: an FPGA that plugs into a USB or serial port and requires a host like the existing systems, or one that can also run as a standalone system, possibly even on a wireless network. Would that be worth another $10-$20 to the price tag?
Adding an SD card interface is almost free. For the cost of a socket (around $3) and a bit of space on the PC board you're done. The SPI interface only needs 4 connections + power. USB (host mode) would be nicer, but somewhat more complex as you'd probably need a USB controller.
If you're going to add an MCU to the board anyway, and if you're considering an ARM processor, then you should know that there are a number of ARM9 processors that include an MMU and can run Linux if you provide them with sufficient amounts of memory. But I suspect you may be looking at MCUs that have fixed amounts of on-board memory which is far short of what is required to run Linux. Actually, I'm curious to know why you'd want to have an external MCU when the FPGA is fully capable of booting itself from compatible flash memory and a soft-CPU equivalent to an AVR32 would use less than a thousand LEs?
The advantage of Linux over rolling your own custom firmware is that it saves you a lot of re-inventing the wheel, especially for standalone operation. It will be *much* faster to develop under the Linux operating system than it would be under Atmel Studio for instance. Linux drivers exist for a lot of hardware (ethernet/sd over spi/usb/etc.) whereas the selection in Atmel Studio (or AVR Codevision for that matter) is much more limited. And what is the added cost anyway? An extra watt of power dissipation? A few dollars in parts?