All in all, the BFA is "good enough" most of the times. For the use cases where it isn't, you're either:
* Budget constrained and can't really afford not using BFA
* Able to (pay for and) use either a color wheel in front of your sensor, or go with prism + triple sensor.
* Bite the bullet and go with a "strange" color array. You'll probably need to work on the software side for demosaicing to get proper support and fix eventual artifacts.
[0] even more green! 20/36 photosites are green, 8 red 8 blue
[1] with W being white, meaning no color filter or "panchromatic cell". In theory this helps on dim light conditions.
More importantly, green is close to what your eyes perceive as luminance. This is important because you can perceive a lot more luma detail than chroma detail. This is why things like 4:2:2 sampling work.
If you read Bayer's original patent, he proposed using Y Cr Cb (luminance, colour part red, colour part blue) instead of GBR filters[0]. This would people optimal from a computer science perspective. Sadly it doesn't work physically. Sensing negative-blue and negative-red can't really be done with a simple filter.