Job Class system (FF series) - Because FF does it best and I'm not going to try to narrow it down cause each of them have their strengths and weaknesses.

Shin Megami Tensei III - Demon collecting aside, the main characters own growth is pretty unique since you acquire special items you equip which not only affect their strength/weakness that can or can't be exploited, but they also teach a variety of spells or abilities that are in correlation with their strengths. The game also incorporates a Pokemon limited skill slot, meaning that once you master eight skills, you'll need to drop one if you want a new one, with close to a hundred skills to choose from, it's easy to build the MC however you want. You also get to choose which stats go up when they level, and like the best RPGs, even though you can only raise one stat, you'll feel the difference pretty quickly.

Breath of Fire III - Hey the Master System is basically FFVI's Esper system all grown up and better balanced. It also has a blue mage mechanic.

Demon's Souls/Dark Souls series - For something that comes across so basic, it's surprisingly deep as your equipment and weapon setup is heavily dependent on your stats. With the sheer variety of builds possible with this game, it's no surprise if has such high replay value.

I'm still trying to think of a fifth one.