I'm a slightly conspiracy-minded person...when it comes to budgets, anyway. I think the lack of a well deck is there simply to drive the requirement for LPDs that have a well deck. "We've got to complete the San Antonio class--how else can we get all this other gear ashore?"
Split-ARG ops are an essential part of MEU missions, IMO. No well deck on the big deck means this is a huge degrader for the ARG to maintain presence for extended duration. The Kearsarge ARG in '98 provided port/starboard TRAP and humanitarian assistance coverage for the Kosovo bombing campaign, as an example. Can't do that unless both halves of the ARG have both air and surface capability.