I don't have enough digital stuff to care about folders, but I think the menu may be faster now, unless it's just my imagination.
Maybe I'll make a "rubbish" folder to place all the useless icons like "Health and Safety" and "Wii U Chat."
As for Wii Mode, I always thought that it exists the way it does for two reasons. One is to ensure 100% compatibility and execution, and two is security reasons to quarantine off homebrew. The Wii is different from DSi so I don't think it could be set up exactly the same way, even something like a passthrough might be risky from Nintendo's view.
But hey, it's still a lot easier than playing any PS3 game on a PS4, right?