New games use new antipiracy checks which all sky3ds carts cannot (and will never) pass. These are enabled by the flags at 0x1FE in the NCSD header. FE:IF and the new Animal Crossing both use these new checks, but whoever dumped AC did a shit job by actually zeroing those bits (and consequently invalidating the entire NCSD header, smh.)
I haven't looked into it as far as I'd like to yet, but I'm under the impression these checks come from brand new hardware responses. Think AP2.5 on 360, except a bit tougher since carts are pretty much a black box compared to DVD drives. Sky3ds only ever existed because the protocol on 3DS carts is so simple and has relatively minimal security. Protocol-level (i.e. not just crypto) cart security like this should keep these cart emulator devices away from new games for a good while, thankfully.