You'll have that problem with pretty much any pad. One possible solution is to allow multiple buttons to map onto certain joystick directions.
Then you can have a dedicated jump button, but still keep the normal up direction working as well.
The XBox version of VICE is allowing that, so I have the B button mapped to Up there, which makes those games work nicely.
Also it's kind of useful to map additional buttons to keyboard keys, such as Space. Then you can throw grenades in Commando for example.