Sure, DDR2 will last for more than a few years. Heck, there are still loads of machines with DDR let alone DDR2. But, since you are planning on a new build, I would go with DDR3. Even though latencies are high, it's only a matter of time until latency drops and DDR3 reaches insane speeds. When DDR2 first hit the market the latency was horrible with DDR machines besting DDR2, but that changed as DDR2 became the mainstream, DDR3 will follow the same trend.
All things considered though, I'd wait until next year before fully jumping on the DDR3 bandwagon, until more procs and mobos are on the market that take advantage of DDR3.