Are you sure that there's not a plan to recover the second stage once they've consistently been recovering the first stage? (I'm assuming that would be part of the road-map).
The project's long-term objectives include
returning a launch vehicle first stage to
the launch site in minutes and to return a
second stage to the launch pad following
orbital realignment with the launch site
and atmospheric reentry in up to 24 hours.
Seems way harder for way lower returns to recover the second stage. Only 1 engine instead of 9, and you're recovering from orbital velocity which opens up several new cans of worms. Would they need heat shielding? The extra weight there might blow away any cost savings from recovering the engine.
Heat shielding is needed, as well as extra landing engines that work outside of vacuum, since the second stage engine would destroy itself under atmospheric pressure. It's easy to see how quickly you start to get dimishing returns, but it would be cool if they could pull it off.
Some experiments were done in early 2000 with inflatable aerobrake. The concept was shown to work, but experiments weren't a complete success. However this technology I'm sure can be applied to the task of returning the second stage.
Apparently they are no longer pursuing stage 2 reuse on the Falcon 9. The next gen superheavy lift rocket, the BFR, is intended to be fully reusable though.
If you're going to build an expendable rocket designing it as a SSTO doesn't really make sense. With a single stage you can't shed the extra weight of the engines and rocket that got you out of the atmosphere and have to have engines that work both in atmosphere and in vacuum.
What I was trying to say is that there are other reasons to not build a single stage to orbit expendable rocket, mostly cost and payload capacity. I agree it'd be easier than a reusable version but if you're not returning the stage it makes way more sense to use the 2+ stage designs that are common today. Being able to shed the weight of the atmospheric stage and switch to a vacuum optimized engine is a big benefit.