I use the Saitek F.L.Y. 5 with extra pedals and Track IR and I love it (mostly). The only thing I would wish for is that the spring that centers the stick is a bit hard. Other than that it is the only stick I know of that have dual thrust controls... which I use extensivly in game.
I love the X52 look and feel, but unfortunatly the price is a tad bit to high (compared to the €40 range of the FLY), but the major issue I have is the bulkiness of the X52 and throttle which goes really bad with my desk layout. The FLY on the other hand fits perfectly in my lap so I like it that way too.
I have set my joystick and pedals up in a way that have pretty much eliminated my use of the keyboard entirely (not counting coms and quitting the game). Some functions like cargo scoop I use the ingame interface to enable/disable.
Anyway here is my setup which works for me.
X-Axis > Yaw axis
Y-Axis > Pitch axis
Twist Axis > Lateral thrust axis
Throttle Control 1 > Throttle axis
Throttle Control 2 > Vertical thrust axis
Pedals push> Roll axis
Buttons
1 > Primary fire group, select in interface mode
2 > Secondary fire group
3 > Target highest threat
4 > Target straight ahead
5 > Cycle next hostile
6 > Frame shift drive
7 > Deploy heat sink
8 > Target next subsystem
9 > Target previous subsystem
10 > Speed boost
11 > Toggle landing gear
Pov up > Boost engine, Up in interface mode
Pov right > Boost weapons, next panel tab in interface mode
Pov left > Boost system, previous panel tab in interface mode
Pov down > Balance power, Down in interface mode
Up/down weel up > Deploy/retract hardpoints, Next tab in interface mode
Up/down weel down > Previous tab in interface mode