I don't think there is anything wrong with playing a game of Dom 3 with him. I mean there certainly are some themes I wouldn't want my 5 year old exploring (like previously mentioned blood sacrifices) until he was older and better able to grasp some of the concepts, but a simple game between you and the AI, where you pick the nations involved (and thus are able to reasonably avoid some of the more complex/grimmer themes) would be a pretty good idea. With some adult supervision you could reasonably walk him through and avoid anything you don't want to go into too much detail.
You could explain the basic mechanics to him, let him give you commands that you input into the game, and go turn by turn and let him see how a game unfolds while you answer any questions he might have. Send a bunch of knights at those dragons and if it doesn't work? Maybe suggest a different course of action for him to take.
I know it isn't exactly the same, but at roughly that age I finally broke my dad down and had him teach me how to play Axis & Allies. Sure, at age 6 or 7 I just wanted to play with little plastic tanks and bombers, but it was some great quality time and I was able to start learning things like allocation of resources (few that they were) at an age where most of my friends were playing Mario (not that there is anything wrong with Mario).
You could build some fond memories with the little fella between turns of subjugating the heathens.
