I don't remember Wind Waker having 16:9 support at all. Neither did Twilight Princess.
Some GC games do have Widescreen support, such as I-Ninja, Battalion Wars, Burnout 1 & 2, Eternal Darkness, F-Zero GX, or Lego Star Wars 2. That said, I never used it myself, so I can't tell you if it looks good or not.
The problem with widescreen on the Wii (and well, other systems too), is that it's Anamorphic, which means that the picture is just stretched, and as already mentioned, while you may get a bit more field of view, the picture quality takes a hit, specially text and 2D sprites / HUD-like assets, they become much blurrier, so 4:3 is by far the best mode if you care about picture quality as that's how most games were designed to be seen.
The few games that are "only" 16:9 such as the Kirby games, NSMB Wii o DKCR, aren't really widescreen games either, they just force it because they're 2D platformers with strong multiplayer features (and in fact I force the picture to 4:3 in my TV when I play those, lol). I'd need to replay Xenoblade Chronicles to say something about it.
About Virtual Console, I have no problem with those myself, although I only use the VC for N64 and maybe some neo geo game. I launch those through USB Loader GX with 4:3 forced and they look fine (well, better than fine, because N64 on Wii is uppressed to 480P, so looks better than on original hardware).
For the rest, though, I recommend emulators all the way, I really don't see the point of installing NES/SNES/Mega Drive wads myself when emulators offer so much more. Specially RetroArch-SS, a fantastic fork of RetroArch. While setting it up may take a bit and require some know-how, the end results are worth the time, because, at least tome, RA gives you the best picture quality of pretty much all the emulators I tried, and a great array of options too.