We know GW can be blocked, we aren't sure if Nintendo is able to block the Sky3ds (depends on how it fakes being a real card). So with GW you rely on them to always be able to make a new version emunand (I'm not sure exactly how they do that, so I don't know if they will be able to do it forever). Sky3ds might be blockable, nobody knows. With both you can just stay on the latest usable firmware, but it looks like GW maxes out at 9.20 for now, but until they actually release the 9.2 exploit nobody really knows.
GW has extra capabilities, like CIAs and homebrew, but you have to launch the exploit every time you power down.
Sky3ds doesn't require an exploit, just plug it in any play. It can take a while to cycle through games (Idk if the card remembers the last game you've played if you power down the 3ds, maybe someone else can verify). Sky can't do anything but play roms. Ninty has pushed a few updates since Sky's release and they haven't blocked it yet. Maybe the can, maybe they can't, but I'd bet that Nintendo can't do much about it because they have always been very quick to squash exploits.
Depends on what you want. Plug-and-play solution but only roms, or opening an exploit and relying on emunand for extra capabilities like cias?