I never played GBA games on Wii U because my experience with NES/SNES/N64 titles was so fucking poor. That's the reality. The fact that there might be a difference between platform emulation on Wii U shows you how terrible the VC quality is on Wii U.
I thought it was just NES that had the dark filter?
Here is a SNES comparison between Wii U and SNES Classic from N.E.R.D.
https://youtu.be/fXPEEHOq8aQ