The original DS had no copy protection or DRM other than that it required proprietary cartridges. Once these were understood and reproduced, it was trivial to run code such as the R4 menu.
The 3DS on the other hand is a much more complicated and secure beast. First of all, it actually has an operating system, code signing and firmware updates. This means that short of a hack (like gateway or others) its only possible to run code approved (Signed) by Nintendo. The Sky3ds works by imitating a 3ds game cart EXACTLY which fools the system into running it. That said only games that the 3ds would run ordinarily will work (because they must be signed) which is why it has no region free, homebrew,
cheats or even a menu. The advantage though is that it can work on any firmware because its essentially software independent.
Unfortunately for Sky, Nintendo has been able to strike back with their new anti-piracy features. So far Sky3DS has been completely unable to circumvent this protection while Gateway was able to come up with a fix in less than 24 hours.
These reasons and more are why I think Gateway is the better device by far. Currently the only downside is the lack of updates for N3DS, but I'd be surprised if they didn't have something in the works.
-palantine