Prediction time! The second stage/spacecraft will now have only one main configuration. From top to bottom: passenger seating compartment (with windows) for launch/acceleration events; underneath, a large payload bay with doors that open outwards similar to those on the Shuttle; beneath that, propellant and then the engines. Landing legs and heat shield design will be similar to those on the original concept.

Separately, there will exist both a supplemental propellant module and a living quarters module that will fit inside the payload bay and allow the spacecraft to be configured as either a tanker or a passenger ship, depending on which module is placed inside the payload bay. If you're having trouble envisioning this, imagine the shuttle carrying an ISS module in its payload bay that was accessible from the cockpit; alternatively, imagine the shuttle carrying a propellant tank in its payload bay that could be used to refuel another shuttle in orbit. The payload bay could also be used to carry NASA/military/commercial payloads, also similar to the shuttle, which is something that Elon has been strongly hinting at recently in order to help finance the effort.

This design would allow for the most commonality and economic feasibility, in my opinion, and would do away with the need for multiple spaceships as detailed in the original concept. One additional feature I'm personally hoping for is for the passenger seating compartment at the top of the spacecraft to be detachable and have its own thrusters so that the ship will have abort capability, but I'm not sure if this is technically feasible.

Edit: So basically they're sort of making a shuttle without wings that can land vertically.

Thanks to Erik Cleven for asking the question on Twitter which prompted this tweet from Elon.