hm actually this other board i don’t think does a lot for you as far as approximating the aleph. it comes with SDRAM instead of SRAM, so the heap memory is much bigger and slower. RS232 port would still needs conversion to serial-usb (aleph uses a slaved AVR8 running LUFA for this; older monome devices used FTDI.) ethernet would go unused (unless networking is part of your vision.)
we don’t use any extra flash in the aleph beyond the internal 512k. (bees app stores everything on the sdcard - in hindsight more flash would probably have been a good idea; as it is we should at some point redo the scenes structuring to be more space-efficient and store the default scene+module internally.)
so my 2 cents would be: if you want to use avr32 go with the barebones version and build on it from there.
or maybe you have something else lying around that could serve as an initial testing controller. for example, an Arduino Uno would work fine - it has USB host capabilities and SPI, and is easy to program.