pangya fantasy golf (psp/windows), outlaw golf (gc/windows), kirby's dream course (snes), super swing golf (wii) and nes open (nes)
have you tried ff tactics or ogre battle/tactics ogre?
other games that come to mind:
legend of legaia
parasite eve (more upgrading guns though)
vagrant story
star ocean: the second story
and by default, I have to recommend xenogears (but it's not so much skill mastery points as mastering skills through proficiency).