Depends on how Nintendo optimized their emulators: since they release each ROM file separately, they can always customize/hack the emulator for a particular game
, which homebrew emulators generally don't do.
They can also patch games and includes precalculated game data or textures (like N64 VC emulator is doing).
However, except maybe SNES and GBA, all emulators are running every games full speed and I would say they are also often more accurate (regarding sound/video) that their VC counterparts because the original emulator author (not speaking about those who ported them on Wii) put many years and a lot of efforts in them...
In all case, they offer lot more options (not hard to do since VC does not have ANY options) which is a big advantage.
Regarding estethical aspects, which seems to be the most appealing feature of VC WADS for noobs, I'd say it doesn't matter once you are playing the game, which is what is was done for
And I don't see how VC are more polished (except the banner maybe, which you only see on startup so what's the big deal ?), they don't even have a fully featured menu, contrary to most emulators. E-manual does not count, they look like shit and I never used them.
For people who are too lazy to launch the homebrew channel or just want direct acces, there are emulato wads as well, forwarder or not. I think it would also be possible to inject a ROM into an homebrew emulator and make it launch automatically, I've already done this during the gamecube good old time
Then there are those just excited at seeing all their wads dancing in the system menu