Like most things pitching related, it is all about "feel", some are more comfortable from the wind up, while others prefer pitching from the stretch. All things being equal - whether you are coming out of leg lift from the stretch, or wind up, there really is very negligible, to no real advantage to the actual wind up, other than as stated before maybe some "style" points. If there are mechanical differences, then you will see a difference.
With young pitchers, I prefer to have them only from the stretch. Jr. has never pitched from the wind up, and early on he really thought he was "weird" because everyone had this big ole wind up with no runners on base, and he wasn't allowed to. Now he doesn't give it a second thought. Being a LHP, for him there is really never any reason to throw from the wind up.
My thoughts on pitching has always been, less equals more, the more movements you have, the more opportunity to get out of sequence, and mechanics break down. Less moving parts equals - more repeatable mechanics, without loss in velocity, in fact if you can repeatably sequence easier with less moving parts, then you will have more velocity. Look at Fernando Rodney - hardly even has any leg kick, yet gets it up there in the mid to upper 90's.