Yes Spycraft can work for a GI Joe game, I did so in a tabletop though I also added in some of the rules stuff but not setting stuff from the D20 version of Stargate. (D20 Stargate and Spycraft were pretty close to identical already.)
It worked fairly well not the exact feel I wanted but as close as I have been able to get to what I was looking for. (What I was looking for was basically the Larry Hama written Marvel GI Joe comic in role playing form.)
Now if you are aiming for emulating Cartoon GI Joe go with any edition of Cartoon Action Hour since emulating 80s cartoons is the main goal of that game and it does it well.