Quite a few HOTAS systems can combine the joystick, throttle, pedals (and Logitech 940 has that by default) into a single Windows device. CH certainly can do that (a capability that I really love), and high end Thrustmasters should as well.
A search for HOTAS in this forum led me to believe it wasn't quite that simple ...
http://www.hard-light.net/forums/index.php?topic=84413.msg1685921#msg1685921 not with Thrustmaster at least.
Not sure about Logitech either, but interesting that it works this way for CH.
Newer games of course don't have that issue. (Can easily bind all functions in Elite:Dangerous for instance.)
Ironically I specifically choose the X55 because it allows for each device to be connected directly by USB completely independent of each other, without any cable between throttle and stick, which always annoyed me with other setups I had.