I'm not in favour of this kind of thing, sure it could have potential to be a great thing, but I think it would just be overly complex having to switch between programs, and would cut people out who didn't like other genre/s used. If someone wanted to do it though, good luck to them.
The other program would have to be free, or it would drastically slash the player base.
And finally, I think two or more protagonists would have to be used. I suppose you could set it up so that the player is the greatest man on the planet and can do anything, but ideally, you'd want more than one person. Ace lands his ship on the enemy ship, and then Sgt. Rock jumps out to kick some ass.