They should have addressed it much earlier, but it makes way more sense in historical context: when MySQL added utf8 support in early 2003, the utf8 standard originally permitted up to 6 bytes per char at that time. This had excessive storage implications, and emoji weren't in widespread use at all at the time. 3 bytes were sufficient to store the majority of chars in use at that time, so that's what they went with.

And once they made that choice, there was no easy fix that was also backwards-compatible. MySQL avoids breaking binary data compatibility across upgrades: aside from a few special cases like fractional time support, an upgrade doesn't require rebuilding any of your tables.