I tend to use 2D for most of the time, but switch to 3D when I'm looking at something specific, such as a particular aircraft on approach, or when a helicopter is doing "interesting" manouvers. I probably use 3D about 5% of the time.
If you can afford it, then it's worth while. But you will need to tune the various 3D settings to the capabilities of your PC. IMO, it's best to start with Hardware Flights on MAXIMUM, and Network Flights on MINIMUM - works well on my dual-core Pentium 2.8GHz. Unless you have a super-fast PC, beware of using MAXIMUM on Network Flights.