've been pondering whether it would be possible to create i.e. a 030/040 compatible but more compact and energy efficient turbo card for the A1200 that would fit nicely inside the standard desktop case?
If you did a board that ran totally at 3.3V then it would use less power. Freescale make a few 3V 68K's... I havent looked but as the 68060's core is 3.3V I bet the IO bank could be run at 3.3V too.
You would just need some buffers that can drive a TTL signal and accept 5V logic levels.
As for sticking an FPGA on board for SCSI or SD, yup it could be done, opencores.org have a few designs as do Xilinx and lattice. (Heck a PIC can interface to an SD card)
As for making a more compact card... well I dunno, unless you can get some of the old 208 pin QFP 68060's that are out of production now the 060 is always going to stand tall.
The rest of the logic would be surface mount and chips in the TSSOP and TQFP packages stand only a few mm off the board. Space wise adding connectors is what takes up the space, mount the memory on to the PCB (8 chips normally) and you would save yourself a bit of space.
You could go mad and do a 8 or 10 layer PCB and make a card that looks more like the Amijoe was, a card full of chips with the tracks routed on the layers below but then your talking about a lot of expense.
I would say KISS, 3.3V the CPU board, mount some SD-Ram on the board itself (available from Digikey) and if you want SD card readers or SCSI why not add a USB host chip and use that? I think the overall cost of such a board would be low, except the 060, but you could sell it with a socket so people could hunt around, ripping Atari's to shreds for the 060 ;-)