This kind of difference between real world and theoretical results is quite common. Nothing in your office or home, or even the test bench, will ever run as fast as its design specifications call for.
That said, I was surprised to see USB 3.0 do as poorly as it did. Mind you, it's still much faster than USB 2.0 and somewhat faster than eSATA in data reads. I had expected better from it. I strongly suspect that as USB 3.0 devices and drivers mature, it's speed will significantly improve.
USB 3.0 does have some other advantages over eSATA. For example, like USB 2.0, you can power devices through a USB 3.0 connection, while you'll need another power connection for external eSATA devices.
In addition, USB 3.0, which can handle up to 50% more power than USB 2.0, should be thriftier with energy than 2.0. Alas, it's not. As Brian Nadel reported in ITworld's sister publication Computerworld, current USB 3.0 implementations will drain your laptop's battery faster than their equivalent USB 2.0 devices. Again, the next generation of devices and drivers should handle this better.
Another noteworthy point is that while USB 3.0 is backwards compatible with USB 2.0 cables and devices, you can't use a USB 3.0 cable with a USB 2.0 or earlier device. In addition, you can't use any USB 3.0 device with a USB 2.0 cable. That's because while the flat USB Type A plug, the one that goes into your PC, is compatible with USB 2.0 ports even though it has an extra pair of connectors, the other end is a different story entirely. The Type B plug, which is the one that you use to connect devices to the computer, comes in two different varieties. Neither of these will fit into a USB 2.0 B port.
So, what should you do? If I were you, I'd stand pat for now. USB 3.0 is the wave of the future. Later this year, as the technology matures, USB 3.0 devices should be consistently faster than today's eSATA devices, but we're not there yet.
In addition, for now, you'll still pay a premium for USB 3.0 devices, boards with USB 3.0 ports, and even PCs with USB 3.0 built-in. Towards the year's end though USB 3.0 will become the default on almost all PCS and peripherals. Much as I like USB 3.0, I don't see any reason to hurry up and adopt it today. I'd advise you to wait too.