I have had some interesting conversations with those looking to clone EZ4s. It looks like we find ourselves at the start of when programmable chips and such like were starting to be protected. Not half the trouble it might be to clone a modern chip (early protection was not the best) but not a trivial matter either. Add this on top of difficulties in sourcing chips (the EZ4, despite being one of the last designs out there, is still now some 7 years old and was not exactly built with the latest parts back then) and I am not sure straight cloning is the way forward. Doubly so considering if you do clone you will likely be operating with a binary blob of CPLD code.
I have also long been contemplating a project to make a GBA flash cart as well -- unlike most other consoles there was nothing truly exotic* added to GBA carts if you ignore the RTC and tilt sensors (
http://nocash.emubase.de/gbatek.htm#gbacartridges or
http://nocash.emubase.de/gbatek.htm#gbacartrealtimeclockrtc and keep scrolling).
*NES has mappers, SNES has extra chips, the GB/GBC has fairly extensive bankswitching setups aka
MBC/memory bank controllers, the megadrive had a few things though was not as bad as the others mentioned (some bankswitching for a small handful of games and there was the multiple ports in stuff like micromachines), the N64 had the whole CIC thing and it kind of goes on. The only problem is the GBA cart is memory mapped and requires high speed memory (read basically not NAND, even modern NAND) but that problem is largely solved (use NOR or RAM of some form).
Basic homebrew NOR carts have been made
http://www.ziegler.desaign.de/GBA/gba.htm details a few and a bit more besides.
Multirom on NOR, assuming you can crack the save issue*, is just multiple pages and a reset command. I imagine it is not all that different for NAND-NOR and NAND-PSRAM arrangements (load, point and shoot).
*assuming you are patching to SRAM then the same page setting method you use for the NOR would work, however in practice I have seen various groups patch games to use a different location in the SRAM (it addresses quite a bit if it has to) and have them all nest.
I am not nearly a good enough electrical engineer to jump right into making a full on "EZ4 and then some" level flash cart though. To that end I would probably have to start with a basic single ROM NOR cart and iterate many times.
My one deviation from that would be that I do consider it almost vital to move away from SRAM patching and into emulation (FPGA driven most likely) of the save type -- it was already done by the early DS slot flash carts so doing it in 2013 would be even nicer. Whether you really want to emulate RTC or not I will leave for others to debate.
More curiously though I saw a thread where people were using the 3 in 1 (which is somewhat similar to the EZ4 which in turn is similar to the EZ3 before it) where they were cannibalising them for parts (more specifically the PSRAM). It might just have been someone seeking a pin for pin/protocol compatible thing but I do want to note it.
That said I am willing to help design cases, fiddle with software (I know GBA patching, GBA AP (ish or at least enough assembly to make myself useful) and the GBA hardware) and will offer to critique PCB designs if you want.
For an added bonus the GBA cart is visible in DS memory (you can access it from DS homebrew) and as long as you have something cable of multiboot (which is to say just find a GBA or an SP) then you also have the multiboot protocol to help develop things.