Still, what if there are legitimate 2 letter searches, like for "Ur" as someone else pointed out?
The only way to make mysql index shorter words is by recompiling and setting MIN_WORD_LEN to a different number. They claim that changing this variable from the current value of 4 to 0 will enlarge the index by a factor of 20. So maybe we should go with 2. After that, the indexes have to be rebuilt.
Axel