Has this hacking other games included assembly hacking to any serious level? I ask mainly as here are not many terribly usable compilers for the NES or GB/GBC -- some have gone just beyond the proof of concept stage but where you could happily write C all day long for the GBA you would struggle on anything 16 bit or older for that, slim possible exception for the Amiga. This is not just "oh if it was for real I would have to do some inline assembly" but more "I am limited to non real time things and possibly text adventures".
For my sensibilities/mindset I would probably go with the GB/GBC as the almost Z80 stuff it uses I know more of it than the 6502. Both are simple enough and very popular embedded devices though. Each has hardware enhancements to improve the memory/storage it has (NES mappers and GB/GBC memory bank controllers aka MBCs) and I would probably favour the GB/GBC again here.
In the end it would six of one, half a dozen or another unless you want to play it on hardware, in which case I would say GB/GBC flash carts are probably marginally more developed than NES ones. Though in both cases it would amount to see what everdrive are doing for the console in question at this point in time. Above all that though I would say make it for the PC if this is your first -- nice debugging, nice tools and you can happily make something that looks like it would have been on the NES or GB/GBC. If you want it as a learning project for the hardware then OK but if you are more interested in making a game then don't do this as your first.