RPG Elements

I was listening to the Here Be Gamers podcast today, and i ran across Nathan's description on an "indie" game. It prompted me to try to make this a deviation from the norm. Thus I am currently working on integrating some RPG elements into the game. I don't really know how it will work, beyond the fact that you will have a commander sheet and it will have skills and bonuses for your armies and such; maybe even penalties for the other team(s). There will be various templates for it, such as Engineer, and Undead. That's all I really know for now, but suggestions would be great, and more thoughts will come soon.