Landing the second stage is gonna be Hard. That's Hard in the sense that landing the first stage was Easy.
There were a lot of complex challenges about landing the first stage, but nothing that seemed impossible. Figuring out how to control a spent first stage with almost-empty fuel tanks while falling through the atmosphere at supersonic speed and firing a rocket backwards was surely tough. Getting the control systems right to land that stage lightly on a ship when you're almost out of fuel and have too much thrust to hover is also tough. There's no reason to think that either one should be insurmountable though. If you have the budget and the will to run some experiments and trash some hardware, you should be able to figure it out, and SpaceX had and did.
Now for the second stage, there's a fundamentally harder problem of how to slow down the second stage from orbital velocity without making it so heavy to defeat the purpose. I haven't heard any good ideas on that yet.
SpaceX has rather different economics from most of the rest of the aerospace industry - they aren't getting any super-lucrative Government contracts, and depend on making a profit on fixed-price launches to stay alive. They don't need a ton of good PR or political will, as they're depending on the size of their invoices for launches compared to the competition doing their work for them. If I was them, I'd focus like 90% of my spare engineering effort on optimizing the first-stage recovery and relaunch process as much as possible for now. They've proven it can work, and now they gotta make it fast and cheap. This will bring in boatloads of cash to get the company in better shape and help them corner the launch market. Once they've optimized the first-stage reuse process, then they can really focus effort on looking for a way to recover second stages.
They're looking at experimenting with that on the payload-less Falcon Heavy test flight. For operational use, the payload penalty of the extra mass on a second stage is sufficiently high that it seems likely that only on FH flights (and not even all of them) would they have the possibility.
It incredibly expensive, a satellite that could be lift by a Falcon 9 with a first stage only recovery would have to be lifted by a Falcon Heavy if you wanted to recover the second stage. Basically you'd need to almost double the unfueled weight of the second stage with aerodynamic devices that can withstand the re-entry plasma and the heat shield. And then add the extra weight for the de-orbit and re-entry burns. You would probably more than halve the payload capacity. Even at best is borders on not worth it.
Interestingly, now that SpaceX has the X-37 contract, there is the possibility of launching and recovering a re-used first stage and payload, but not the second stage! I guess this almost happened with the Dragon that contained a re-used pressure vessel, but not-quite.
