Commander Keen/WMG

Mortimer McMire is the grandson of Adolf Hitler
Since Keen is the grandson of B.J. Blazkowicz, who fought Hitler in Wolfenstein 3D, so who knows how far the rivalry goes back? It would also explain some of his beliefs.

Molly is dating Billy's older brother
The games mention him having a brother after all. I know there's nothing to support this WMG, but it sure would make Billy and Mortimer's rivalry more interesting if their siblings had the hots for each other (and by interesting, I mean more vomit-inducing for both boys).

Keen is a murderous psychopath who really, really hates the Vorticons
In the first two games, all the Vorticons Keen encounters are soldiers trying to blow up the Earth, and thus fair game. Then you discover in game two that the Vorticon's aren't really evil, they're just under mind control by the Grand Intellect. Unfortunately, you still have to shoot your way through the mothership. Sacrifices have to be made to save the Earth, after all. But then game three rolls around and Keen goes to the Vorticon homeworld to face the Grand Intellect once and for all...but not before rampaging across the entire planet and wantonly slaughtering its inhabitants, including breaking into their houses and schools, killing everything inside (including women and children,) and then eating all their food.