well, to be honest: you didn't provide a lot of information - for example, am I right in guessing that this happening on a Windows OS PC, or Mac or is it on Linux ?
Low loading speed is largely a function of high I/O throughput (i.e. SSD drives), lots of *free* RAM (to avoid swapping) and fairly fast CPU cores (our boot sequence is largely single-threaded).
So depending on your OS and configuration/settings, you may want to run a system monitor to see what's going on.
Overall, this is really a matter of common sense - for example, what about "hot cache" booting, i.e. is startup faster after having run FG at least once ?
What about changing aircraft/airport ?
To see how much of this is related to your startup settings, see the "level 0" startup profile detailed at:
http://wiki.flightgear.org/Howto:Debugging_extreme_lag