I've been using NDUI for a little over two months now and so far it's been a great experience.
The only drawback I've noticed is an issue with keybinds not being saved on all characters.

I have a main profile for my main character which after setting up I've copied all settings to a general alt profile.
I used this profile on all of my alts, but for some reason when I relog to many of these characters, keybinds do not get saved.

The only way I can restore the keybinds (which are accountwide the same for all of my characters) is by typing in /bb and pressing cancel.
This gives me back all the bindings, as long as I don't log out of the character.

Prior to installed NDUI I did a full UI reset, so there's no leftovers from old addons lingering about.

Hotkeys save on blizzad server, never follow addon settings.
You just need to switch all your character sinto account-wide keybind settings.