GBA was M2, not NERD. And both emulators do use dark filters. IIRC, GBA displays with 75% brightness and Nintendo DS with 80% brightness. Both can be tweaked to offer 100% brightness with homebrew, but they don't come that way.
Another consideration with Wii U vs. Wii VC is input lag. N64 VC on Wii U has absolutely miserable input lag, much worse than on original Wii or even the vWii in the Wii U. I've heard similar things about NES and SNES VC, but I'm not super familiar with either on Wii or Wii U because there's simply better options via homebrew. But for N64, I'd personally take the reduced input lag over improved emulation unless the game simply doesn't run right on Wii. GBA and DS Virtual Console are the only platforms where I've never heard anything negative about their handling of input.
In the scheme of things I'd say it's probably something like:
NES: Just use homebrew emulators, they're better than either VC offering.
SNES: Just use homebrew emulators, they're better than either VC offering.
N64: Wii VC for reduced input lag, Wii U VC for more accurate emulation and rumble support. Homebrew emulator Not64 for most accurate emulation, but N64 is hit and miss--some games work on Not64 but not on Wii/U VC and vice versa. There's no "one size" solution for N64 on Wii/U.
Going back to the OP's question, community emulators are far more accurate than anything the VC has ever done. bsnes would not be remotely possible on Wii U performance-wise. Virtual Console starts with the primary goal of making those emulators run a specific subset of games at 100% speed on very weak hardware, whereas something like bsnes started with the goal of emulating the SNES as accurately as possible, with performance a distant second priority, and performance on low-end hardware like a Wii not even a consideration at all. Genesis Plus (before GX) started with performance as a priority but the Wii (and later libretro) GX port was more of a full rewrite to target accuracy within the limits of the Wii. Something like BlastEm, another community Mega Drive/Genesis emulator, is more accurate again than Wii VC.