IMO, as an engineer, the problems are largely thermal due to packaging. When my friend brought his EFI 390 Berg home I had a close look and told him to expect issues. My Cannondale, despite its many flaws, had a very reliable system once properly insulated. Cheap to fix with off the shelf parts (no $500 fuel pump). The reason the in tank pumps die in these bikes is they cavitate in the boiling gas from a tank right over a super hot header. A two stroke would not have this problem, or a four stroke with an external fuel module(pump/regulator/filter).
I like the simplicty of a carb, and agree on bypassing the EFI two stroke, but would trade it for the power and lack of a large pipe that DI would allow.