1. Boiling extract tends to darken it, so if you prefer a lighter color beer the late extract addition will give a lighter color end result.
2. Less bittering hops are required since your boil will be lower gravity. This can save some money.
I've never heard anyone recommend against the late extract addition. But in theory, the extract that is added as part of a late extract addition misses the original "hot break" at the beginning of the boil, so that some of the proteins don't coagulate as you might like. But it sounds as though this isn't a concern anymore since you get very little hot break material from extracts made now-a-days.