As I see it, the advantages are that once 10.4 is released, GW will stop working in that version (because of the exploit patched) but sky and QQ3DS pro will work since they use cartdridge emulation (more or less) and, if a new anti piracy check is released, they could be updated to bypass it. So, the main advantage is working in the last sysnand version.
Technically GW will shortly work in the latest sysnand as well (since 10.4 isn't released yet). Realistically it will take months/years for stores to have mostly 10.4 systems so I can't see sky/qq3ds being viable anymore