There are a couple threads that talk about the hesitation. In the X3 forums, there seems to be a "known issue" for it (same 3.0 engine).

I thought it was just the X5 3.0 but during my 4.8 test drive, it was present as well. I guess it has to be chalked up to the electronic throttle. I'm also wondering if it can be tuned better by software updates.

How many miles on the car?