3 bolt systems just by their bolt hole pattern being spread in three directions allow for stiffer soles which make for less loss of power in the transfer from rider to pedals.

2 bolt systems on the same design shoe with the same sole will have more flex which is where the power gets lost.

2 bolt systems being more compact allowed for more tread so you can walk. They also allow for a sole design that sheds mud better. That and some other things is probably why they are favored by mountain bikers and they came to be known as mountain bike cleats.

I only ride road bikes. I use 2 bolt spd's. I want to be able to walk without looking like a duck or slipping and busting my butt as I saw one rider do when the got off his bike to snap a quick picture from the roadside.

However the last time I went to the bike store and talked to the salesman about shoes, he told me things have been changing and 3-bolt systems are now easier to walk in. Don't know myself though.