For some, STT still is the easiest way in. I fly a nonstop direct flight from JFK and are off the plane by 12:30. Arrange taxis ahead, hop the ferries and are enjoying evening dinner on VG. I enjoy the ferry rides and the fact that in one day I'm there. I've done alot more miserable things in my life besides standing in a customs line.
So for us, San Juan>beef>VG makes absolutely no sense. I would never NOT route through STT.