I don't know enough about how this all works to really contribute on the subject beyond adding concerns.My only concern is the entirely possible Anti Piracy. If they do that, we're pretty much screwed right? Since you can't edit the roms and then run them.
Last gen Gamefreak fit in AntiPiracy measures for different regions of the games which needed to be patched out. If things are like you said an we can't patch roms that'd be a problem. But is it a problem of it can't be done or they just haven't done it yet? This I don't know the answer to.
I also don't know if the Gateway's operations have been revealed to Gamefreak enough that they could build against it before printing cartridges and I don't know if they could AP it on a guess. The Animal Crossing save problem exists but if it was Pokemon they might have worked or been working harder to crack it if it's possible at all (I don't know much about flash types like NAND). Gateway seeing returns on its first sales now. If it can run Pokemon it'll probably see another wave of sales beyond the risk takers.
So much "wait and see" antsy-ness on my end. This month is going to be a long one.