Do you hold the controller very tightly? I personally get hand discomfort/cramps if i use a keyboard and mouse combo so i'm surprised you are getting them on controller. It might really help people to offer suggestions if you posted your UI? Are you taking advantage of the expanded hotbars?
for the record i used a trusty old dual shock for XI and 1.0 but come 2.0 I switched to an XBox style because of compatibility issues back then, i like the shape because i have long fingers and it offered a wider grip, you might consider it yourself, the official wired microsoft xbox 360 one is rather inexpensive ($29 here from a computer store)