I personally prefer the original Gateway logo. It looks cleaner and more in line with the Nintendo 3DS image.
I particularly don't like the way they made the omega symbol resemble a skull. It connotes that the Gateway software is a virus or harmful in some way. This seems to be a bit inappropriate, particularly in light of the recent bricking fiasco.
Personally I think it would have made more sense to make the omega symbol look like a doorway, portal, or keyhole of some sort to match the brand name.
Maybe it's just me, but I would have also preferred the Menu Splash Screen to at least resemble the stickers on the Gateway Flash Cart itself.