Basically, yes. USB 3.0 has much faster transfer rates than USB 2.0, so if you buy a USB 2.0 drive now you may risk getting the itch to switch to a drive with a faster connection a year or two down the line.
Note that a USB 3.0 drive will still work at USB 2.0 speeds if you connect it to a computer that only has USB 2.0 ports on it. So if you don't have USB 3.0 ports on your computer today, then you won't see any difference today. But you will see a significant difference if you use the drive with a new computer in the future or if you spend perhaps $40 to $50 to buy a USB 3.0 adapter card for your existing computer.
If you plan to use eSATA instead of USB then it may be a non-issue, since eSATA (like USB 3.0) is a lot faster than the drive itself is capable of anyway. But eSATA has cable length restrictions (24" if I recall correctly) that may be too limiting for you.