If you have two joysticks you should install them both. I don't see any reason not to, unless having the joystick centered is really that important to you.
You didn't even ask the interesting question though, which is what type of joystick is best. 4 way? 8 way? 4/8 way switchable? Physically restricted or logically? Analog with lots of maps to emulate 4 way and 8 way? What about 2 way games?
I have an idea for an insert into a control panel top that would take an analog joystick (such as an Ultrastik 360) and have some tabs built into the control panel surface that would slide restrictor plates in to make it a 'digital' 8 way, 4 way, or 2 way, in addition to supporting physically unrestricted analog mode.
If you have the time and skill, that is what I would recommend that you do, and then write up some plans on how to make it so the rest of us can enjoy.
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