What will engage them first, because there are different games that emphasize different things.
FATE Accelerated is the first one to come to mind - the rules get out of the way and you can play anything. In any genre - what interests him, FATE can handle it. That said, it may be too little structure. Limitation breeds creativity as well as helps guide. Also it's not my first choice if wargame-like combat is a draw.
There's a whole stream of Powered by the Apocalypse games in various genres. This gives each player a move book which will help them frame what they want to do and provide some of the structure I was mentioning, while also putting your son firmly int he drivers seat to explore what interests him as the GM is less of a plot-master and more of a facilitator in it. However, part of it is rules for relationships and if it's just a him and you that may be a strike against it.
Bubblegumshoe is a kids detective game like the Hardy Boys, Nancy Drew, Encyclopedia Brown, Three Detectives or Scooby Doo that has both easy rules and can work well with only 1 player. Does that genre range interest him or is (s)he looking for a more heroic (and adult) character? Combat is definitely downplayed, with insult wars being just as "deadly" as a fistfight.
Superheroes is often a good genre for kids - it can be four color and deal with shades of grey only at the levels you feel are appropriate, no death or gore needed, and can be played solo, perhaps with an NPC sidekick (who never steals the spotlight!). Sorry, my knowledge of super systems doesn't give me a good feel on which to use for kids, unless you want to circle back to FATE. (Icons I think is a FATE-based one, or just the base FATE Core and download one of the many fan-made free supers expansions.) But there's probably other supers systems suitable for that age range.
One additional point - my kids often will learn/expand skills watching youtube. There's a lot of both RPG primers as well as actual play. If that is something your 12y.o. likes maybe aim them there, first. I'm watching the episode of Tabletop where they play FATE right now.
https://www.youtube.com/watch?v=NOFXtAHg7vU&feature=em-uploademail