It wouldn't matter on any new games if they all adopt the same save tagging that that animal crossing does. You wouldn't even be able to use any dumps of your saves even if you wanted to if save tagging becomes mandatory on any new games. You would be limited to any of the old games that fall under the "untagged saves" SDK, that would be currently roms 1-250 minus animal crossing and the new mario game.
I just wanted to say that, for the record, the NDS Adaptor Plus DOES still extract newer 3DS save data -- I've done so with Fire Emblem, Mario and Luigi: Dream Team, etc. The only game that doesn't work so far is Animal Crossing: New Leaf.