Yep. This new CFW looks to almost eliminate our legacy retail carts except for a few like AC, SSB, XY not sure on those yet.
Not sure on this game but yes GW can only restore 512kb saves and cannot handle 6.x encrypted saves.
I don't think a whole lot of people realize this yet, but this is HUGE in my opinion. Jimskeet is over there now trying it out, I will get to it hopefully tomorrow. Go check it out, read the threads and get a handle on it. I have not used SDF yet but it really doesn't look very complicated and the CFW just goes away on reboot so it is not going to complicate emunand.