The distinction lies in the difference between aesthetics and themes. The games are polar opposites of each other, with Twilight Princess having a very dark aesthetic and relatively light themes, while Wind Waker has a very jovial and energetic look but makes heavy use of themes of bleakness...
I think killing Ilia would have just been stupid. And honestly, I don't get why people call TP the dark one. It's not. I mean, the graphics are dark and muddy, but the game itself is pretty normal. Wind Waker? That **** was dark.