Wow, several brains on it at once!
I gave them my two cents' worth, thanks for posting the link to their survey!
The biggest shortcoming I have seen so far in the "off the shelf" (sort of) kits is the lack of a viable accelerator pump simulation and poor control of the fuel during the waste-spark overlap cycle. The latter causes blued, then burned, pipes, because there is too much fuel coming through the head between cycles. This is caused by having just one injector, like a throttle body, or by having all injectors fire at once, like the Kawasaki 1000 bikes. They had very expensive pipes to mitigate the bluing effect, and we don't have that option.
So, I told the ambitious college kids to please consider that in their design! Hope they do...