I think you need to change it in the PS3 menu (when you hold down the HOME button during gameplay). There should be a 'controller' option that allows you to switch movement from the d-pad to the analog stick, or under a different option but it should be there somewhere. I remember changing it myself.I played the downloadable one from PSN on the PS3 last time(the legacy collection I was playing gave me a download code rather then putting the game on disc). If there was a way to make the analog sticks work I didn't see it. Made the REX fight a PITA(more than it is already).
Maybe the PC version does, since the PC port is now available for digital download.