1. there's minconnect -- I can structure flights so I have time to sleep while in transit. You will never find those in a normal search engine, they try to achieve minimal time. There's also padconnect, if you don't like booking right on MCT -- which is often wise! -- then, as the name suggests, this will add N minutes to the prescribed minimal connection time.

2. As recently revealed by the company http://www.flyertalk.com/forum/27265924-post483.html you can avoid connections in certain countries which can be beneficial for visa purposes or certain personal privacy requirements ( I know a German physics professor who refuses to go to the US because of the fingerprinting. )